The start of the season revolves around Michael attempting to woo Holly and eventually succeeds only for David Wallace to transfer her to another branch forcing the two to end their relationship just when it got started. Meanwhile Jim and Pam become engaged and struggle through the difficulties of a long distance relationship while Pam is studying art in New York. Eventually new boss Charles Miner enters later in the season and causes trouble for Michael. Michael eventually cannot deal with his dictator-like changes and quits to form his own company taking Pam and Ryan with him. The company becomes successful and eventually Dunder-Miflin is forced to buy them out. The season ends with Pam learning she is pregnant.
Over eight weeks of the summer, a Dunder Mifflin weight-loss initiative causes the branch to diet and become obsessed with their weight. Michael pursues a friendship with his new HR rep, Holly. Andy plans his wedding to Angela, while she continues her affair with Dwight. Jim misses Pam who attends art school in New York, and he finally proposes. A disgraced Ryan returns to the Scranton office as a temp.
Following Ryan's recent scandal, Holly holds an ethics seminar. Michael lets everyone speak freely about their unethical behavior at work and Meredith, in particular, causes a rift between Michael and Holly when Meredith admits a supplier gives her discounts on products and steak coupons in exchange for sex. Holly is ostracized by the staff, but when she is humiliated by the head of Human Resources, Michael once again supports her. Meanwhile, Jim makes Dwight comply with the company's "time theft" policy by timing every second of his personal activity.
Michael practices for the birth of Jan’s baby by having Dwight go over possible birthing scenarios. When Jan arrives for the office baby shower, she has already had baby Astrid, excluding Michael from the process, and he feels disconnected from the baby. Meanwhile, Michael pretends to dislike Holly for Jan’s benefit, but Jan senses their connection and asks Michael not to date Holly. Michael goes to Holly for comfort and they agree to date. The separation between Jim and Pam starts to take a toll on their relationship.
Michael and Holly date, have sex in the office and inadvertently lead to the office being robbed. Michael holds an auction to raise money for all the items lost. On Phyllis's advice, Dwight gives Angela an ultimatum to break up with Andy, which she refuses to do. Pam gets a part-time job at corporate to pay for art school, and Jim is further unsettled after Roy insinuates that he is losing her.
When corporate transfers Holly to Nashua, Michael (with Darryl's help) moves her back to New Hampshire. Their plans to continue dating are dashed and they break up, and Darryl teaches Michael to sing the blues. Pam meets Jim's brothers, who pull a prank on Jim, which embarrasses her. Dwight torments Andy by becoming a fan of Cornell University. Pam is embarrassed when she is the only person at corporate wearing a costume on Halloween.
Dwight and Jim are shocked when they receive poor marks on their annual customer survey reports. They learn that Kelly has sabotaged their scores for blowing off her America's Got Talent wrap party. A sympathetic Michael and Kelly relish their discomfort. Through Angela's manipulations, she and Andy book their wedding at Schrute Farms B&B. Pam and Jim spend every minute together using their Bluetooth phones, including Jim overhearing Pam's friend Alex asking her to stay in New York.
CFO David Wallace sends Michael to Winnipeg, Manitoba for business. Andy and Oscar accompany him and become unlikely friends when they drunk dial Angela. Although Michael makes the sale and has a one-night stand, he rebukes David for transferring Holly. Jim counts down the days until Pam gets back from art school; she fails a course but comes back to Scranton anyway. Ryan seduces Kelly, who in turn breaks up with Darryl.
HR Rep Toby returns from Costa Rica, driving Michael insane. He and Dwight attempt to get Toby fired for cause by planting "drugs" (actually caprese salad) in Toby's desk. Pam is upset that someone in the office has made a mess in the microwave and will not clean it up. Jim surprises Pam by buying his parents' old house; despite its '70s decor, Pam loves it. Ryan breaks up with Kelly to travel to Thailand.
The office must spend a $4,300 surplus or lose it in next year's budget. Factions break out and court Michael to get what they want—Oscar and Jim want a new photocopier, Pam, Stanley, and others want new chairs. They finally agree on the chairs to prevent Michael from earning a bonus by returning the surplus. Dwight takes Angela and Andy to Schrute Farms to settle wedding plans. In a mock ceremony, Dwight secretly weds Angela, but she is angered at his deception and plans to have the wedding annulled.
Phyllis's Moroccan-themed Christmas party is interrupted when Meredith's hair catches on fire during a drunken bellydance; Michael stages an intervention and attempts to force Meredith into rehab. Dwight makes a killing selling a popular Christmas toy--"Princess Unicorn." Phyllis continues to torment Angela on the Party Planning Committee. When she revolts, Phyllis shocks everyone by revealing Angela and Dwight's affair to everyone (except Andy).
The office is tense because Andy still hasn't found out about Angela's affair with Dwight. After Michael tells him, Dwight and Andy plan a duel. When they realize Angela has been sleeping with both of them, both dump her. In New York, Michael is called to corporate to meet with David Wallace, who wants to know Michael's methods, as the Scranton branch is actually doing well. Not surprisingly, Michael has no insight.
By request of David Wallace, Michael and Dwight go undercover to investigate rival paper company Prince Paper. As they are a small, family-owned operation made of an extremely nice family, Michael has a difficult time handing over their findings to Wallace. Meanwhile, the rest of the office holds a debate to settle a question: is Hilary Swank hot? The office is tied six to six and the discussion turns heated.
After Dwight's fire safety seminar goes awry, he must make amends to the stressed-out office. Michael tries a number of ways to get his employees to relax before discovering that he is the number one stressor at work. So that people won't feel afraid of him, he insists on a no-holds-barred roast of himself. Also, while watching a pirated movie, Andy is convinced that Jim and Pam are film gurus. Special Guest Stars: Jack Black, Jessica Alba, & Cloris Leachman.
Michael goes on a speaking tour of the other branches to explain Scranton's relative success, accompanied by his driver, Pam. Back at the office, Dwight and Jim—now the heads of the party planning committee—forget a birthday, with severe consequences. Meanwhile, Andy falls for someone he should not.
Michael and Pam continue their tour of the branches with Michael taking a lesson from their visit to Utica. Dwight and Jim struggle to fulfill their new party planning duties with a grumpy staff. Angela's new cat causes a stir.
The blood drive comes to the office on Valentine's Day. Jim and Pam have an awkward lunch with Bob Vance and Phyllis. Michael meets a lovely girl but when he cannot find her, he sets up a Valentine's Day party with his friends.
Michael Scott has a great idea to promote business. As "Willy Wonka" Michael puts Golden Tickets into different paper for discounts. When a huge company gets all of the tickets, Michael has to find a way out of this mess.
Loyal manager Michael has been working for Dunder Mifflin for 15 years and is going to have a party. The new vice president, Charles Miner, comes and Michael does not like how strict he is. He shuts down the party and gets on bad terms with Jim. Michael rushes to Corporate to meet with the president. The president reluctantly agrees with Michael but this manager has had enough. Michael Scott QUITS the Office!
After quitting, Michael Scott has two weeks notice. He starts goofing off more than ever. Michael decides to steal customers for a new paper company but is caught by Charles Miner and thrown out. Michael sneaks back in and tries to steal employees but no one follows him. Vice President Charles Miner assigns Stanley as Productivity Czar and Kevin as the temporary receptionist because Pam joins Michael as a salesman in The Michael Scott Paper Company.
The Michael Scott Paper Company is open for business! With the aid of Pam, Vicrum, and Ryan, Michael sets out to get his business off the ground. With a meeting set up with an investment club, and Bob the Building Manager, will Michael be able to start his company, or will he regret his decision to leave Dunder Mifflin? Meanwhile, back at The Office, Jim and Charles square off for a battle of the wills, in a good old-fashioned game of soccer. Winner takes all!
Michael, Pam and Ryan chafe working in such close quarters. After hosting a Paper & Pancakes luncheon, they are about to call it quits when Pam makes her first sale for the company. Dwight's and Andy's unlikely friendship is tested when they are both attracted to the new receptionist Erin. Jim spends his day trying to figure out what Charles means by his requested "run down". Includes an alternate title sequence featuring The Michael Scott Paper Company.
Dwight, finding a new hero in Charles, clashes with Michael as each tries to steal the other's clients. After trying to sell Jim and Pam on his failed wedding plans, Andy tries to provide for all of Jim's emotional needs. Jim takes the opportunity to prank Andy, but also reassures him he will find love again.
Jim learns Charles is a suckup while Charles finally recognizes Dwight's bizarre personality. Although Michael, Pam and Ryan have landed a number of clients, they learn their company's business model will not sustain beyond a month and they will fail. David Wallace investigates the seeming success of Michael's company, and Michael, Pam and Ryan hide their failure long enough to engineer a buyout. Michael is given his old job back, and Pam and Ryan are given jobs in sales.
Michael mediates a dispute over customers between "new employees" Pam and Ryan and the others on the sales team. Pam and Ryan are forced to return the customers and with fewer customers, Michael is forced to fire one of them. Meanwhile, Toby confronts several employees who take the term casual Fridays too loosely.
To break the staff of the focus Charles instilled in them, Michael opens a café-disco in the downstairs office to release stress. While initially resistant, all the staff (even Angela) join as Kelly and Andy bond in a dance-off. Pam and Jim plan to elope but later reconsider. Phyllis suspects Bob will have an affair with his new secretary.
At the annual Dunder Mifflin company picnic, Michael and Holly are reunited. They perform a skit where they inappropriately announce the closing of the Buffalo branch, but Michael fails to tell her that he loves her. The Scranton branch plays well in the volleyball tournament. While getting an x-ray for a sprained ankle, Pam and Jim learn that she is expecting.