Pedro's health is beginning to deteriorate, as his T-cell count gets lower. The cast is beginning to realize the extent of his illness and is worried about the possible consequences. This creates tension between Pedro and Puck, because Puck does not respect the way Pedro chooses to live his life. Pedro continues to give educational seminars on living with HIV and Pam and Judd go to support him when he speaks at Stanford University. Rachel and Cory go with Puck to the house he grew up in and meet his mother, who, to their surprise, is completely normal. The next day, Pedro, Judd and Pam go to the park and take it easy by playing soccer and enjoying each other's company.

As the group enjoys their last few days together, Cory, Judd, Pam and Pedro spend a day in Monterey while Rachel and Jo bond in San Francisco. Mo continues to work hard on his band's single and music video, isolating himself from his roommates. Pedro and Rachel have lunch and discuss their different views in life. Despite their differences they seem to understand each other's viewpoints and remain friends. Puck gets his driver's license back, picks up his car, and heads to the Lombard loft to pick up some of his things he left behind when he was kicked out. The entire casts, minus Puck, sit around and play a question and answer game. As move-out day arrives, they all reflect on how this experience has changed them and eventually hugs and tears follow. Jo and Rachel are the last to leave, but not before one more phone call from…you guessed it, Puck. Puck talks to Rachel about their relationship when they first moved in. When the group finally leaves, the house that eight strangers calle

The Rachel/Puck flirtation continues with the Critical Mass bike ride, leaving Judd on the outside of the triangle. Pedro overhears Puck and Rachel telling gay jokes on the phone; he gets upset, but lets it go. Pedro grapples with the fear that his relationship with Sean is going to fast, he tells Pam that he's falling in love. Rachel tries to go out on a date with Harlow, but Puck winds up chaperoning and interfering, leading to Rachel's decision to distance herself from Puck. Rachel's friends, Patty, Francis and Heather come to visit. Judd gets romantic with Francis, but is saddened when she returns to Arizona. Puck's constant flirtation with Heather leads to an argument between Rachel and Heather. Rachel denies any attraction to Puck. Pedro talks to Sean about feeling torn between Sean/San Francisco and family/Miami. Puck assures Rachel that nothing happened with Heather.

Aloha! The cast leaves for an adventure in Hawaii, where they hope that they'll have a chance to bond. Once they arrive there is trouble in paradise as the group fights over the suite. Once they are all settled in, they head off to a luau. A vegan, Jo gets very disturbed when the roasted pig is pulled out of the ground. She feels that the stuffed pig looks like a rotten corpse. Jo accidentally eats some of the pork and runs to the bathroom. The cast tries surfing and the girls rock, while the guys have trouble. Pedro has plenty of time to relax and enjoys parasailing. Jo and Rachel bond by partying and meeting guys. While the cast is cliff diving, Rachel slips off the cliff. Luckily, she makes it down in one piece. By the end of the trip the group is closer and the friendships grow stronger.

Bruno's estranged brother, who he has not spoken to in three years, visits, and the roommates witness Bruno's temper.

A hookup between Jenn and Peter has major repercussions; Tyara is her own worst enemy in her relationship with Theo.

The roommates go through hard times. Cory can't find a job. She treks all over San Francisco and nobody will hire her. The girls struggle together: Pam is working hard on her medical school projects, while Rachel is waiting to hear about her grad school applications. Puck finds a dog and grows very attached to his new four-legged friend. The roommates convince Puck to do the right thing and find the owner. Deep down, Puck is a nice guy. He searches high and low to find the lucky owners of the dog.

Puck getting the boot from the house was named number 97 on TV Guide/ TV Lands 100 Memorable TV Moments in December of 2004.

Everyone seems to be enjoying Puck's absence and the chemistry among the cast has drastically improved. Pedro goes home with Rachel to Phoenix and visits her very religious family. While there, Pedro gives another educational seminar on having HIV at the junior high where Rachel's father works. After looking at the pictures Rachel brings home, her mother is not happy with her actions in San Francisco, namely the piercing of her belly button. It is also Pam's birthday and her boyfriend Christopher flies in to surprise her. Christopher stays hidden until the rest of the cast performs a ""This is your life Pam"" skit and Christopher shows up at the very end. They all celebrate her birthday by skiing in Tahoe.

Judd tries to find work cartooning but is frustrated at every turn, until he gets invited to pitch his idea in Hollywood. Mo works with his band and he and Puck get into an argument about rap music. As soon as Judd starts to get closer to his confidante, Pam, her boyfriend, Chris, arrives in town. At the Bammie Awards--the ""Grammys"" for the Bay Area--the roommates ogle rockers while Mo mingles to promote his band. All go to see Mo's band perform at the Gavin Convention. Judd makes a second trip to the San Francisco Examiner and comes away with the job of weekly cartoonist.

Pedro and Sean want to take their relationship to the next level and decide to exchange vows. Pedro's friend Alex flies in from Miami for the party and tries to convince the two to move to Miami. The three bond and later Alex realizes that Pedro and Sean are happy together where they are. While Sean and Pedro prepare for their new life, the exiled Puck talks about his relationship with Toni, and how he can see them together for the rest of their lives. Back at the house the group fixes up the pad for the big day as Puck continues to bug them with phone calls. With congratulatory speeches from Pam, Judd, and Alex, Pedro and Sean exchange rings and seal their love with a kiss.

Cory and Puck are spending a lot of time together and having fun as friends. Pedro and Puck are the ""odd couple."" Puck insults Pedro all the time because Pedro is gay. Pedro voices his frustrations about Puck to the roommates. Pedro decides to separate himself from all the roommates as long as Puck is around. Pedro goes home to visit his family. Back at the house. Puck explains his opinion on how people need to be worthy to earn his respect. Tension builds in the house when the cast asks each other personal questions.

Dom is faced with his parent's mortality when he returns home to Ireland to visit his ailing father. Dom's visit has a rehabilitating affect on his father. Dom goes drinking with his sister, Barbara, and his cousin, Peter; they lose track of time and make up an unbelievable story to explain for their tardiness. The roommates note Jon's personality changes. They watch as a scared Jon competes in a country music competition at the Borderline Bar; he wins the first round.

The roomies are growing irritated with Puck. They are annoyed with his disrespect for the rest of the cast and his complete selfishness in any given situation. Puck meets a woman named Toni at the park and goes on a few dates with her. She even accompanies him to the hair salon when he decides to dye his hair blue. Everyone but Puck goes out to dinner for Mohammed's birthday and they all come to the conclusion that something needs to be done about Puck. They begin to confront him and he immediately gets defensive, which forces them to decide whether or not having him stay in the house is really worth all this trouble.

The roommates are growing close to Jo. They feel that Jo is a positive influence in the house. She has great new ideas and an adventurous personality. Jo takes the roommates rock climbing. Rachel achieves a great feat and climbs to the top of the rocks. Judd has been spending time with a good friend from college named Jessica. He wants the relationship to move to a romantic level. Meanwhile, Jo receives bad news from Steve. He notifies her that she must appear in court because her ex-husband is appealing her restraining order. Jo is emotionally stressed and frustrated, but Cory is right there to support her through it all. Judd and Rachel decide to go out for a night on the town. They pretend to be a couple so they will seem more attractive. Jo begins to bond very closely with Cory. A non-confrontational person, Jo loves the house because everyone has so much respect for each other and is so supportive of her.

Tony is shocked when two of his Skeletons move in, creating a battle for his affection between them and Madison.

Puck invites his fellow roommates to a screening of his soapbox derby video and is hurt when no one attends except Rachel. Judd shows his romantic side and goes on a date with Jeannie but no sparks fly. The whole group gets embroiled in a dinner argument with Puck which seems to focus on ""90210,"" but really is about his overall attitude and actions. Puck explains his history and his home. Puck skips Pedro's birthday breakfast in retaliation for the soapbox snub, then he confronts Cory about the same thing, resulting in renewed appreciation. The arrival of Puck's pit bull, Joker, provides a way for all to see a new side of Puck.

Pedro and Sean's relationship has been on the rocks, and Pedro feels that he needs to get away. He heads to Miami to visit his family, where he feels at home. Pedro hangs out with his two best friends to unwind. During his visit home, Pedro gets very ill. He visits a doctor and tries to get lots of rest. His family and roommates are all very worried about Pedro's health. Cory and Puck spend time together to reflect on the house situation. Puck feels that the roommates care more about Pedro than him. Pedro confronts Cory about their misunderstandings.

Pedro's health weakens and he is sent to the emergency room with a temperature of 104 degrees. The cast begins to realize the full extent of his sickness and tries not to let it bother them that he is getting closer and closer to the end of his life. A confused Mohammed breaks up with Stephanie, hooks up with a friend from San Diego, then calls Stephanie crying and tries to repair what is left of their relationship. To take a break from all of the drama in their lives, the group goes horseback riding.

Puck reappears in this episode as he calls the group to invite them to a party. None of the cast members show up but a few days later, while at a bar with Judd, a drunken Rachel calls Puck to invite him down there for some drinks. After fighting as usual, Rachel storms off and vows never talk to Puck again. This vow is then broken soon after as he calls to try and repair the damage. The two meet in a park only to fight, yet again, about the cast's reasoning for kicking him out of the house. This dispute initiates the search for a new roommate and after interviewing three individuals, the group decides on Jo, a young woman from London. Jo's friend Steve takes Cory and Rachel rock climbing soon after she moves in, which helps break the ice between the cast members and Jo.

As the New York cast envisions the future of their successors, Dom, Tami and Jon make their way across the country in a motor home. Heather predicts that someone will leave early. Dominic, one of the new blood, expects no problems at all. Dominic and Tami arrive in Owensboro to pick up Jon and are immediately taken aback by his very ""country"" lifestyle. Dominic is most amazed by Jon's popularity at a local club, where he sings ""Boot Scootin' Boogie."" Jon worries about Dom's drinking habits, while Dom is unnerved that Jon doesn't drink at all. Jon objects when Tami asks the Magic 8 Ball, ""Will Jon get laid?"" He is very uncomfortable discussing his sex life and says that he doesn't believe in sex before marriage. Jon talks about how his parents reacted to Tami and Dom and offend both of them. Jon backs off, trying to maintain some civility during the road trip.

Beth causes a huge rift in the tentative friendship among the roommates when she brings all of them, including Dominic--who initially does not want to go--to a party that she wasn't even invited to. The roommates are asked to leave and everyone blames Beth. Dominic criticizes her for humiliating them. This spat occurs after Dominic confronts Beth about bringing her cat into the house without permission. The friction between them lessens as they begin to truly talk with each other. Meanwhile, the relationship between David and Jon becomes strained as they begin to realize how different they are. An argument about the mess left on the porch leads to David physically attacking Jon, which Aaron breaks up.

Beth S.'s history is related through her discussions with her roommates and her mother's visit to the loft. Jon observes Beth S. on the phone with an ex-boyfriend and steps in when things get uncomfortable. On arrival, Beth S.'s mom cleans the house and fixes a typical Polish meal for the roommates. Jon discovers more about the relationship between Beth S. and her mom through a private dinner them. Glen and Beth S. bicker at dinner and Jon talks with Glen and Aaron about picking on Beth S. Aaron confronts Beth S. about the disrespect he has shown towards her, while she confronts Glen, who admits that their relationship needs work. Beth S. wins everyone's respect when she beats them all at paintball.

A group visit to the Upper Room poetry reading featuring Mohammed leaves Cory feeling dull and ordinary. Each of the roommates' career pursuits is examined as Cory tries to find her niche in life. Rachel's political views are expressed after a trip to a Jack Kemp rally, which leads to an argument with Mohammed, leaving Rachel hurt. Pedro has his first date with Sean. Cory unintentionally offends Mo's girlfriend Stephanie by asking if she's half white. The group finds a new way to communicate when Mo organizes a poetry night at the house.

The cast is back from their island adventure and Rachel has decided to join ""Empower America,"" a conservative Republican group. The cast accompanies her to the seminar and Judd and Rachel get into an argument later about the supposed ""racism"" that goes on in the group. Rachel decides to get a tattoo on her lower back, which conflicts with her ""conservative beliefs,"" making the cast question her behavior. Tensions rise between Cory and Rachel because Cory begins to get jealous of the friendship developing between Rachel and Jo. Cory pouts around the house when Rachel and Jo bring home some skater friends and she later confronts Rachel with her issues. Steve starts to make Jo feel trapped as he calls her every day and tells her he is expecting that they will eventually date. She completely moves out of his house in Tahoe to ease the tension.