Pam and Toby are shown to have a good relationship. Pam has shown much displeasure at Michael's harsh treatment of Toby. Toby has had a crush on Pam ever since she called off her wedding with Roy and Jim went to Stamford, but he is too shy to tell her his feelings. In "Cocktails" Toby spends his whole evening trying to win a stuffed animal duck at a claw machine for her. When he finally wins, Pam gives back the stuffed animal and says "Don't you have a daughter?". In "Dunder Mifflin Infinity" Toby is the first to find out about Jim and Pam's relationship, by seeing her kiss him on the cheek in the break room. Upset about Pam's new relationship, he sends out a memo asking for no "PDA" in the office. In the episode "Business School," Pam asks Toby to come to her art show, and he says he can't make it because of his daughter's play. He then gets really upset and yells, "Damn it!" and questions if maybe he doesn't have to go to see his daughter's play and instead could go see Pam's art show.
In "Night Out," Pam thinks that a joke that Toby told was funny, and he gets really excited and touches her awkwardly on the leg. She did not appear to be angered at this. After an awkward silence, Toby announces his move to Costa Rica. In "Goodbye, Toby" Pam gives to Toby an office picture of the staff that excludes her (because she took the picture herself) for when he leaves for Costa Rica. Toby, unsatisfied by the lack of her presence, shouts at the office staff asking for a camera (possibly the loudest he's ever spoken). When no one responds, he runs off for an extended amount of time just to find a camera to have a picture of her and him together. Pam also helps Toby take revenge against Michael in this episode after his insulting farewell gift is exposed during a meeting and she gets him to unwillingly give up his watch to Toby, which he does (Pam potentially may have disclosed Michael's abuse of Toby if he didn't do what she said). At the end of the episode, Pam comments (though not to Toby) that she always thought he was kind of cute and that she will miss him a lot. In "Niagara" Toby appears to still have feelings for Pam and is happy when they run out on their wedding. He is later disappointed when the wedding is called back on but is seen smiling and clapping after they're married and run down the aisle. During "Roy's Wedding", while Jim and Pam are trying to find out if there's anything they don't know about each other, Toby correctly answers facts about Pam. Everyone notices him, and Toby, clearly embarrassed, attempts to cover it up. There have been a few occasions when Pam has mistreated Toby somewhat such as hanging up on him on the phone after asking him for help and also hitting him in the eye with a paper airplane and getting angry at him for crossing and does not apologize and simply asks whether she is still in the contest despite injuring Toby. In the series finale, while dancing with Pam, Toby began sobbing. Pam questions Toby with "Is it me? Is it Nellie?" Toby shakes his head, and responds with "It's everything." Pam then hugs Toby as he weeps.
Jim mentions that when he first started working at Dunder Mifflin, he shared a cubicle with Toby and that the two of them got along well. Michael moved them apart because he thought that the two talked too much. In deleted scenes from The Fire and Take Your Daughter to Work Day it's implied that Toby and Jim are friends and Jim babysits Toby's daughter on occasion. When Jim becomes Co-Regional Manager with Michael in season six, however, Jim almost begins to mirror Michael's treatment of Toby somewhat. In "The Lover", when Toby casually says "Hey Jim", a stressed Jim snaps "Not now Toby! My God!" leaving Toby bewildered and hurt, though it is more likely Jim did this due to being angered upon learning that Michael is dating Pam's mother behind their backs and also snapped at Michael in the conversation shortly after. In the earlier "Survivor Man", Jim also says about Toby "He's great, but sometimes he can be a little bit much," showing that he sees Toby as being annoying sometimes. Jim was aware of Toby's crush on Pam but never seemed very bothered by it. However, Toby would occasionally be bitter towards Jim, as seen in "Did I Stutter?" where he assists Ryan (now Vice President) in giving Jim a formal warning for his job performance. During "Stairmageddon", Jim turns to Toby for advice on marriage counselling due to Toby's past of going to such counselling. Jim is left thoughtful and concerned when Toby notes that Pam is in a very difficult situation of short-term vs. long-term issues with Jim's work at Athleap. Despite the moments mentioned above, Jim and Toby have a decent relationship.
Kelly and Ryan
Toby shares the Annex with Kelly, and he is exasperated at being in the close proximity of Kelly and Ryan's juvenile romantic escapades. Using the excuse that he was allergic to his desk, Toby moved locations to escape Kelly's constant talking, moving out of the cubicle, albeit only to a desk adjacent to it. Toby later wonders if Michael intentionally moved Ryan to his former area in order to torture him via Ryan and Kelly's endless fighting, commenting that "If he did... genius." Kelly stated in a deleted scene from Goodbye, Toby that she was attracted to Toby but could not stand "his stupid kid" and was visibly downcast when he announced his plans to leave the office and move to Costa Rica. Toby overall has a good relationship with both Kelly and Ryan and the two have never mistreated him in any way and once even attempted to encourage him to punch Michael in "Frame Toby", possibly showing that they are disgusted at Michael's harsh treatment of Toby.
In a deleted scene from "Ben Franklin," when warehouse foreman Darryl Philbin is told that Michael has sent Toby home to prevent him from interfering with the hiring of a stripper, Darryl refers to Toby ("that red-haired guy with the sad eyes") as a cool guy. While on a trip to the Corporate offices with Darryl and Michael in "The Negotiation," Darryl also offers to let Toby crash for the night at a relative's house in New York, denying Michael the same opportunity. He also had a nickname for Toby ("T-dog") at one point, though their relationship soured when Dwight's plan to expose Darryl's worker's compensation fraud led to embarrassment for all of them and Toby insulted Darryl and his sister. Despite this, the two seem to have a good relationship and Darryl once kindly gave Toby his Christmas doll to give to his daughter Sasha.
Toby and Andy did not appear to have any major disputes when Andy was a salesman or during his first year as manager and seemed to have a good relationship. In "New Guys", when Toby shoots down Andy's intention to make up a cause to fire Nellie Bertram, Andy responds "now I know why Michael hated you so much". Toby appeared dismayed at this. Andy later ridiculed both Toby and Nellie during the slack-lining later in the episode. Andy continued his irritability in "Work Bus" when asking Toby "how are you not murdered every hour", suggesting he, like Michael and Jim before him, has inherited the typical manager's disdain for Toby. Andy was occasionally nasty to Toby on a few other occasions as well and even groped Toby before quitting Dunder Mifflin.
Toby appeared aware of Andy's poor treatment of Erin as a girlfriend, which he pointed out to Nellie in "Customer Loyalty". In the finale, however, after Andy returns with a more positive and friendly attitude, Toby is pleased to hear him (and several other staff members) encourage him to join them at the after party in the warehouse, implying the two are now on good terms.
Toby and Dwight appear to have a stable relationship and Dwight does not appear to hate Toby like Michael does, though on a few occasions Dwight has helped Michael make Toby miserable such as trying to get him fired once he returned from his vacation from Costa Rica and stealing a Christmas present from him on Michael's orders. Dwight also made no attempt to help Toby when he was selling Christmas dolls and ran out just as Toby asked for one for his daughter. Dwight has also on a few occasions laughed at Michael's insults towards Toby but has also shown some displeasure when Michael takes it too far such as in "Goodbye Toby," where he himself admits that he thought Michael's idea to give Toby a rock as a goodbye present was over the line. It is likely that Dwight makes Toby miserable due to his loyalty to Michael. The two have gotten along on a few occasions and it is revealed that Dwight complains to Toby all the time about Jim's pranks against him and once made a deal with him to sign a petition of his in exchange for cookies from Toby's daughter. Toby and Dwight also share an interest in trains during a conversation while spying on Darryl and Dwight says he is welcome anytime to come to his farm. Toby has on occasion been stern with Dwight such as in "Casual Friday," in which he threatened to write him up if he didn't sit down and has foiled some of Dwight's dangerous schemes such as leaving weapons in the office and stopping Dwight from wearing dangerous costumes to Halloween (for which Dwight threatens to kill him). In the final episode of the series, Dwight fires Toby alongside Kevin, possibly indicating that he dislikes Toby and that he annoys him to a degree, like his predecessors Michael, Jim, and Andy (or possibly on orders from Corporate or to prevent him from interfering in his firing of Kevin). While Dwight states that he misses Kevin after firing him, he never states the same for Toby. Dwight does, however, invite him to his wedding, possibly showing that he does consider him a friend.
In "Get the Girl" Toby introduces himself to Nellie as Tony, to which Pam replies "You messed up saying your name?" He answers her by saying, "It happens, okay?"
In "Dwight Christmas", at the office Christmas party, Nellie expressed interest upon hearing that Toby had been a juror in the Scranton Strangler case. He proceeds to bore her, however, with a long, drawn-out account that is implied to have lasted for several hours. Nellie finally leans in close and shushes him. A puzzled Toby then asks if she is about to kiss him. Attempting to save face, Nellie gives him a small kiss, which causes an emboldened Toby to give her a much more passionate kiss.
Toby does not appear in the two subsequent episodes, during which the events of the party are not referenced. In "Customer Loyalty", however, he appears very tactile and affectionate towards Nellie, apparently under the impression that the two are now in a relationship. Nellie, for her part, had forgotten the kiss until that point and finds Toby's affection somewhat awkward.
In "Moving On", Nellie gets fed up with Toby's constant hand-wringing over the possible non-guilt of the convicted Scranton Strangler and pushes him to visit the man in prison; when the Strangler proves he is the killer and nearly kills Toby himself, Nellie admits Toby was brave and a speechless Toby (his larynx was injured by the Strangler) looks happy. However, Nellie later firmly establishes her contempt for Toby and there is no further romantic story-line between them. She is also somewhat rude and insulting to him on a few occasions notably in "Paper Airplane" in which she speaks of him as being a loser, however, Nellie's poor treatment of him could stem from Toby's awkward and annoying behaviour towards her.
When Toby returns to Scranton for the reunion and Angela & Dwight's wedding, Nellie (also returning to Scranton from her new home in Poland) lets the camera crew know she isn't thrilled about seeing Toby again. At the airport, Nellie rebuffs an attempted hug from Toby, snidely brushes aside his comment about a relationship she ended by saying she un-followed him on Facebook and questions him of how long he's been stalking her (Toby quietly says anyone can read non-protected tweets) and declines his offer to share a cab into town. After that point, Toby has no further interactions of any kind with Nellie.
Pete and Clark
After the departure of Kelly and Ryan, Toby appears more excited with the arrival of the two twenty-somethings who are single like himself. He appears to see them as closer friends than they see him but neither of them treats him meanly either. He convinced both of them, along with Kevin and Darryl, to grow moustaches from "Movember", believing this was a bonding activity. He was disappointed when Pete shaved his moustache off after Erin found it off-putting.
Toby appears to consider Pete a better fit for Erin than Andy, largely because he doesn't appreciate Andy's belittling treatment of him and also because he never had any romantic interest in Erin. At the documentary reunion, Pete is nice to Toby and is visibly happy when Toby decides to attend an after-party he had been planning to skip.
Toby only appears in a few episodes, showing up first in a scene in "Diversity Day," in which he jokes about sitting in an Indian Circle (to which everyone else laughs). Michael, having told many more offensive jokes, is offended by Toby's joke and tells him that "This is an environment of welcoming, and you should just get the hell out of here." Toby does so and the staff suddenly goes very quiet. This is the first instance in the relationship between the two, Toby trying to be responsible, and Michael trying to demean and undermine him as much as possible. In "Hot Girl," Toby is introduced by Michael to Katy the purse saleswoman; after Toby and Katy begin talking happily about their high school days, Michael deliberately humiliates Toby by mentioning his divorce and how he once briefly had to live in his car. He also notices the picture of Toby's daughter on his desk, and refers to her as "cute"; however, this is probably a further attempt to portray Toby, a divorced father, as undesirable.
One of Toby's major appearances was in "Sexual Harassment," where he holds a Sexual Harassment Meeting for the staff, only to be interrupted by Michael and a blow-up doll. Michael then states that everyone is still "generally quite happy," which he thinks is because Toby has not yet had the meeting. In fact, Toby did have the meeting and everyone clapped after he was done, leaving them in a good mood.
In a deleted scene of "Halloween," Toby tries to persuade Michael to make a decision as to which employee he must fire. When Michael chooses Toby, Toby replies that he does not report to Michael. When Michael then tries to get Toby to quit, Toby replies that someone else will just take his place. Michael then claims that if he had the authority, he would immediately fire Toby, to which Toby calmly replies, "I know, Michael."
In "Booze Cruise," Toby is late arriving at the dock for a company cruise. When Michael orders the ship to leave without him, Toby grins broadly, implying he had planned things in order to miss the event.
In "Take Your Daughter to Work Day," Toby's daughter, Sasha, distracts Michael; the two actually get along, showing Michael's friendly side. Toby and Michael have a good conversation about Michael's desire to have a family: Michael wants to have a biological child, and Toby hints that he should seek out alternatives. When Michael asks if Sasha already has a godfather, Toby quickly replies, "Yes."
"Conflict Resolution" is by far Toby's biggest role in the season. Toby shows that he handles inter-office complaints calmly and efficiently, only to see his work undone by Michael's stupidity. When Dwight threatens to quit unless Michael fires Jim (because of Jim's history of pranks against Dwight), Michael attempts to resolve the conflict by making vague promises of future action, an approach similar to one Toby had used successfully in the past. Toby covertly shows that he files Dwight's complaints against Jim in a trash box and that he puts the huge number of complaints against Michael in unmarked boxes that are filed into the vast space of the warehouse.
In "Casino Night," Toby tries to convince Michael not to invite Boy Scouts to a company Casino Night. Michael's response is to demean him in front of everybody. Toby just lets him finish. That night, however, Toby viciously beats Michael at no-limit Texas Hold 'Em, to Michael's visible irritation. Later, Toby says to the camera, "I'm not gonna lie—it felt good to take money from Michael. I'm gonna chase that feeling."
In "The Convention," after finding out that Pam is no longer engaged, Toby makes a couple of attempts to ask her out but can't say the words. Michael trashes Toby to Jim and eagerly asks Jim if the HR rep is the reason he left for Stamford. Michael is visibly stung when Jim says no (he later tells Michael about his declaration of love for Pam).
In "The Convict," Michael jokingly refers to Toby as a rapist, much to the dismay of those present. Later, Toby convinces Michael to release the office employees from the conference room, whom he had locked in there as punishment for unfavorably comparing Dunder Mifflin to a prison.
In "A Benihana Christmas," Michael has Dwight take Toby's gift bag present of an expensive robe when they run out of enough of them for everyone. Pam later comes over and kindly gives her robe to Toby.
In "Back from Vacation," Toby asks Michael about the "Jamaica Jan Sun Princess" photo. Michael tries to accuse Toby of stealing the file from him, but Toby says "nine different people sent it to me, including my ex-wife, and, well, we don't talk." Michael then insults Toby's divorce again and calls him a perv, but does state for the record that he and Jan do not have a relationship.
In "Phyllis' Wedding" Toby is seen with a beautiful woman whom he says he met in the gym, although Kevin believes she is a paid escort. When Phyllis tosses her bouquet, it is Toby's date that catches it, and then excitedly runs back to Toby and the two share a brief embrace and kiss. Toby is then shown in a talking head as very ecstatic towards the outcome. It is implied that Toby and his date eventually broke up afterwards as this is the only episode where she is seen.
In "Business School" he tells Pam he cannot make it to her art show because his daughter has a play. He then offers to miss his daughter's play because "what they do is not art."
In "Cocktails" Toby spends the whole evening trying to win Pam a duck from a claw machine after she comments on how cute it is. When he finally wins it, Pam suggests that he give it to his daughter instead.
In "The Negotiation," Toby is forced to listen to Ryan and Kelly bickering nonstop when Michael moves Ryan back to the annex. Toby wonders if Michael did this to punish Toby and that if he did, it was a genius move. Toby goes with Michael and Darryl to New York after Jan says she will not do the contract negotiation unless Toby is there. When Michael repeatedly mentions his and Jan's relationship at that point, Toby takes notes and Michael insults him, but Toby just says he's "preparing for the deposition" that he thinks will inevitably occur because Michael threatened to withhold sex from a female superior in order to get a modest, scheduled raise, commenting, "It will be a groundbreaking case when it inevitably goes to trial." Additionally, when Darryl says he will stay in New York for the night, he tells Toby he can join him and stay at his relative's house, pointedly not extending the same offer to Michael.
In "Women's Appreciation," Toby is out of the office at a parent-teacher conference when Phyllis is flashed. When he returns, Michael scoffs at his alibi and seriously asks to see his penis to rule him out as a suspect. Toby turns towards Michael and looks like he's about to get angry; Michael then seems to catch himself and admits what he said to Toby was wrong.
In "Beach Games," Michael bans Toby from attending the beach event because he wants it to be fun and says it will not be if Toby is there. Toby is visibly upset that he will not get to see Pam in a bikini (which she ends up not wearing there) and is seen despondently doing paper work in a deleted scene from the episode.
On the Season 3 DVD, Toby gives a series of wraparound interviews. Among other things:
- He lists the various insulting nicknames Michael has for him, including "The Devil's Butthole" and "Gargamel", noting "I prefer Toby".
- He describes Michael's "invention" of a safe George Foreman Grill after he burned his foot, which involved putting the Grill inside a bunny cage.
- He says that his job is not a nightmare because you wake up from nightmares; it's more like an unrelenting "daymare."
- He lists what he would do if he had one day to live, including wanting to "Burn this place (The Office) to the ground" this makes the interviewer react with horror and/or disbelief which Toby responds to with a confused "What?".
- He says, "HR isn't just a job, it's a way of life. (Pause) But I wish it was just a job."
In "Fun Run" Toby goes against Michael's theory of an office curse by mentioning he won a drawing at a local pizza place, but Michael insults him and later ignores his statement that you cannot ask employees about their religions. Before the race, Dwight puts Imodium in Toby's drink instead of Ex-Lax and Michael pulls Toby's shorts down right before the starting gun is fired. Toby later wins the race to cure rabies, beating Michael and accomplishing something noteworthy; however, no one notices his win, and Kelly does not even bother looking up when he crosses the finish line. Toby then wonders why the 5K course was a straight line instead of a circle that would have returned everyone to the Dunder Mifflin building.
In "Dunder Mifflin Infinity" after Toby sees Pam kiss Jim he sends out a memo about Public Display of Affection. When Michael accosts Toby about the memo (thinking it's about him and Jan having sex in the office), Toby tells him, in front of everyone, that it is about Jim and Pam. When they confirm that they are dating everyone is happy, except Toby. Later Pam and Jim visit him to see if they have to sign a "Love Contract," but he tells them to wait and see. In a scene that was added to the episode's repeat airing on NBC, Toby comes into work with a woman he says is his girlfriend and makes out with her right in front of the reception desk and Pam.
In "Money" Toby shows that he uses very good grammar when he corrects Michael and clears up a confusion between the usages of the words "whoever" and "whomever" ("who" is used as a subject, while "whom" is used as an object). Michael responds by telling Toby to shove a letter opener in his skull.
In a deleted scene of "Local Ad," Toby pitches an idea of having a stop motion ad that Michael, of course, puts down although the rest of the office seems to like the idea. When the local ad is being played at the bar, Toby is in the ad, but only briefly. While Michael was shooting the scene of the paper airplane flying out of the hand of Creed towards the conference room window, you see Toby in the conference room packing up whatever work he was finishing. Michael did not want Toby in the video; however, for a fleeting moment, Toby had managed to unintentionally get a part in the ad.
Toby's distaste for Pam's relationship with Jim is again brought up in "Branch Wars" when Jim is allowed to join "The Finer Things Club," an exclusive organization built up by Pam, Toby, and Oscar, dedicated to discussing civilized culture. During the episode's final scene, after Jim contributes his ideas on the book being discussed, Toby scrutinizes him very bitterly, hinting again at his disdain for Jim's success with Pam. His irritation is attributed to the fact that Jim did not read the book, though Oscar and even Pam are also annoyed with Jim's wisecracking, uninformed behavior. Also in this episode Michael tells Karen she can have Toby instead of Stanley; when Karen says Toby is not a salesperson, Michael briefly tries to talk up Toby's ability to learn before saying he can't fake it and insulting the HR rep anew.
In the episode "Survivor Man," Toby ends up getting on Jim's nerves. When Jim is named Acting Manager while Michael is off on his "wilderness adventure" and starts altering the office's birthday schedule, Toby asks Jim if he can have a birthday celebration, explaining that Michael deliberately held a party for Toby at 4:58 PM on a Friday so no one would attend. Jim agrees but comments that he likes Toby but that the guy is really annoying him. Jim's dismissive, disgusted attitude toward Toby (whom he has always gotten along with before) very closely mirrors how Michael treats Toby. It is not clear whether Jim is genuinely fed up with Toby or whether this interplay showed that Jim was beginning to act like Michael. It is also possible that Jim was not annoyed at Toby specifically but at the general reaction to his plan.
Michael's hatred for Toby is brought up again in "The Deposition" when Michael says he does not want Toby in the deposition and nastily asks if the HR rep is there "to renew your divorce vows" (Toby is also sitting a conspicuous distance from Michael in the uncrowded room being used for the proceedings). When the two happen to sit next to each other at lunch, Toby kindly tells Michael that he can relate to Michael's situation, of Toby's parents' divorce. While Toby is talking, Michael pushes Toby's lunch tray on the floor, then gets up and leaves. Later in the episode, Toby begins to laugh at Michael after learning Michael thinks Ryan is "hot." Also, after Jan's attorney brings out Michael's diary, and the head of the deposition says "Okay, we'll need ten copies of that diary," to which Toby says, "Make that eleven." In a deleted scene, Michael asks Toby if he will tell Meredith that the car accident from Fun Run was Michael's fault, and Toby nods.
In the episode "Night Out," he puts his hand on Pam's leg and caresses it for a long, awkward moment, which everyone standing around seems to notice, making this the first time the employees see Toby's possible crush on Pam. Immediately thereafter, realizing what he had just done, he abruptly announces that he is moving to Costa Rica, runs outside to the security fence, scales it, and disappears into the night. This scene was done by a stunt double, as Lieberstein wanted to do it himself but it was decided for insurance reasons to let the stuntman do his work.
In "Did I Stutter?," Toby and Ryan together (who both have a problem with Jim; Toby dislikes him for dating Pam and Ryan dislikes him for going over his head) warn Jim on his job performance, citing specifically his indifference toward his job and use of time (namely "goofing off with Dwight" and "time spent at Reception" with Pam). Toby then says to the camera that Jim's time spent with Pam "has finally caught up to him," but he repeats Pam's name several times when unnecessary. Toby later says, though, that he agrees that Jim has good numbers but Ryan thinks they are not good enough. In the same episode, Toby convinces Michael he needs to deal with Stanley for his open insubordination during a staff meeting, though Michael goes about it a different way because Toby's method "did not work because it was stupid." Michael also says Toby does not have any friends, but Michael does so in the context of stating that Stanley is Michael's friend, which is later shown to be completely inaccurate. It is also shown that Dwight thinks Toby may be Jewish, as Dwight's org chart shows a blue Star of David with a question mark next to Toby's name; Toby did not say what (if any) religion he practiced when Michael prodded the staffers to talk about their religious practices in Fun Run. As Toby spent time in a seminary (as revealed in season five episode "Casual Friday,") he is most likely a Roman Catholic.
In "Goodbye, Toby", he follows through on his earlier plans and quits his job as HR representative to move to Costa Rica. Michael is overjoyed at his departure and plans to throw a lavish goodbye party that reflects this. Both Kelly and Pam say they are sorry he is leaving, with Pam saying in an interview that she thinks he's kind of cute. Toby also ends up annoying Holly, his replacement, to a degree while showing her around the office and she is somewhat rude to him and claims that he almost bored her to sleep, something which Michael enjoys hearing (Holly remains oblivious that Michael, in fact, abuses Toby and Michael claims that Toby tortures him). Toby faces a cruel exit interview from Michael but the tables are turned when Holly and Pam join the interview. Michael is unable to berate Toby at length as Holly takes over. When she asks Toby; "How can Dunder Mifflin be improved?," Toby claims he has a few ideas. Realizing that Toby has a potential opportunity to complain about his behavior and abuse, Michael hides his face and angrily glares at Toby, threatening to kill him if he answers the question. Toby does not seem afraid but simply gives a "things are OK as they are" answer. Toby later tells the camera that he has survived Michael's abuse long enough and that disclosing it is pointless. Toby gets revenge when Michael's insulting farewell gift to him is exposed and Pam gets Michael to give up his watch to Toby, which he does, clearly upset. Toby's main concern on his last day is getting pictures of himself alone with Pam, which he finally does as his party is ending. Michael gets a last dig in by having Hank the security guard escort Toby out of the office as he leaves for his new life in Costa Rica. In a deleted scene at his farewell party, Toby refers to an undefined incident involving his sister; this marks the first time Toby has mentioned having any siblings, although late in season 7 he reveals also having a brother Rory.
In season five, Toby is revealed to be in traction in a Costa Rican hospital, with a broken neck, after a zip-line accident on his third day in Costa Rica. He explains that he has yet to see the beach, but expresses some happiness with the camera crew for visiting. He also implies in an earlier talk with Oscar that he is attracted to a woman who is visiting a nearby resort with her husband, thus continuing his tendency to fall for unavailable women à la Pam. In a deleted scene from Baby Shower, Toby can be heard on the speakerphone with Holly, noting that he enjoys his stay at the hospital more than his treatment from Michael at the office.
In "Frame Toby" it is revealed that Toby had returned to the office for a week without Michael noticing. When the staff tells Michael that Toby is back, Michael thinks it's a joke until he sees Toby and screams "No God! Please No! No!" Michael asks David Wallace to get rid of Toby but the CFO says he can not fire Toby without cause. Michael then attempts to get Toby fired by giving Pam a fake letter to give to Toby, asking him to hug and kiss her no matter how much she resisted, and taunting the HR rep into punching him, but both plans fail. Michael then tries out Dwight's idea of planting drugs in Toby's desk (unknowingly buying basil from a caprese salad from warehouse workers who he thinks sold him marijuana). However, he does feel guilty about what he has done and, when the police are investigating the "drugs," Michael tells the police that it's a mistake and tries to stop them from arresting Toby. This suggests that, while Michael does hate Toby, there are limits to his hatred. Then again, Toby's reaction to the setup—that it wasted the cops' time that could have been used to deal with law enforcement—inspires more shock and disgust from Michael.
He is seen on occasion in the background in the "Annex" of the office. When Michael gives his two weeks notice, Toby shows he's not as resentful towards Michael as Michael is to him in a talking head, referring to him as a movie on an airplane, which is nothing special but something to watch. He was seen breaking up a jam session in the lunch room up between Dwight and Andy who were attempting to impress the new receptionist with guitar and banjo to the song "Take Me Home, Country Roads" by John Denver. Toby simply says, "You have to stop."
In "Stress Relief", Toby is seen attempting to help the others escape Dwight's fire drill. In the second part of the episode, during the roasting of Michael, Toby begins to walk to the mike but Michael stops him declaring that only friends are allowed to roast him and Toby agrees and sits back down and laughs with the rest of the audience at Michael being roasted. It is possible Michael stopped Toby from roasting him not only because they are not friends but because Toby would have the worst things to say about him.
He is also involved in the episode "Casual Friday" where he has a talking head about his beginnings at Dunder Mifflin. He used to be in seminary, but he left because he wanted to have sex with a girl named Kathy and took the HR job at Dunder Mifflin so he could be with her. Kathy is revealed to be the name of his ex-wife, and he does not appear to have a passion for HR. In the same episode, he has to deal with complaints about a too relaxed dress code by Oscar and Meredith. For the first time, he is stern with his employees and enforces HR policy by cancelling Casual Fridays at the office.
In the episode "Gossip" Michael spreads rumors about various people throughout the Office, including that Toby is a virgin, even though he has a daughter.
In the episode "The Meeting", Dwight and Toby investigate a dishonest workman's compensation claim filed by Darryl, an event which results in Dwight and Darryl filing complaints against each other, leaving Toby to "drown in a sea of paperwork." During the episode, Toby ends up bonding with Dwight when they share an interest in trains, and finds that Dwight is restoring a life size one in his slaughterhouse.
Although he does not appear, directly, in the episode The Promotion, Michael and Jim put baked beans on pictures of the employees as a way to decide the raises. Jim then sees a drawn picture of what looks to be a clown with a caption saying "I'm an idiot" and asks Michael who it is, Michael answers, saying it is Toby. Jim reminds Michael that Toby is not part of this and Michael answers "I just wanted to draw a picture of him".
In the episode "Niagara", Toby kindly offers Michael the second bed he has in his room but Michael insults him by telling him he will be sleeping alone for the rest of his life and walks away. Toby seems to at least have some feelings left for Pam, as he seems to be happy when reacting to a possibility of Jim and Pam's wedding being called off. When the wedding does go on, however, he is seen dancing with the others and cheering Jim and Pam on as they walk down the aisle at the ceremony's end.
In the following episode, "Mafia", Oscar comments that with Jim and Pam off on their honeymoon and Toby having "mentally checked out in June" he is the only person left to counter insane antics with rational thinking. When hearing of Oscar's comments Toby casually agrees with him.
In the episode "The Lover", Toby is yelled at by both Michael and Jim when he walks in on them just after Michael has told Jim he's dating Pam's mom. Later, after Pam blew up at Michael in the conference during an office meeting, Michael comes to Toby desperate to make Pam happy about his relationship with her mother. Toby offers to talk to Pam for Michael and Michael even goes as far as hugging Toby and calls him a good good-guy. Toby is extremely happy at the hope that things will finally change between them that he says "you know I always knew that if Michael just took the time to get to know me, we would be friends." But once Toby is unable to smooth things over, Michael dismisses Toby as a jackass and goes right back to hating him.
In the episode "Koi Pond", Toby is present in the meeting where Michael wants to talk about insults in the office and as usual when Toby simply makes a point Michael insults him by calling him a waste of life, though corrects himself claiming that's what he would like to say but the meeting is an insult free zone. However, when Michael reveals he has fallen into two fountains Toby appears to find this funny and laughs at Michael. After this, he asks for Michael to kick him out of the meeting and Michael tells him to go.
In the episode "Double Date", Toby talks to Pam to make sure she plans on hitting Michael off grounds. He then gives Pam some tips on how to punch harder, even going through motions with her on how to do it as Michael watches on from his office, visibly afraid.
In the episode "Secret Santa', Toby is called "Antichrist" for calling Michael's Jesus costume inappropriate. In "The Banker" Toby is interviewed by an investment banker as he evaluates the branch. Michael tries to have Toby distracted while Dwight impersonates him but Toby appears and makes Dwight leave. Despite knowing of several questionable incidents that have taken place in the office, he does not say anything to the banker. He expresses his torn feelings about this in a talking head.
In "Whistleblower", Toby is revealed to have written a few chapters of a mystery novel and receives advice on the plot from Jo Bennett to which he replies in an interview, "Write your own damn novel!"