Wil did not appear in any episodes from Season 1 to Season 2.
He first appeared in "The Creepy Candy Coating Corollary" as he enters the Mystic Warlords of Ka'a tournament with Stuart and playing against Sheldon and Raj. Sheldon only joined because he wanted to confront him over an incident of the past: a young 15 year old Sheldon was devastated when Wheaton Wesley Crusher failed to show up at the '95 Dixie Trek convention in Jackson, Mississippi (it is later revealed in "The Russian Rocket Reaction" that Wil attended Hollywood Squares instead). In the final match, Sheldon is about to defeat his hated rival, but Wheaton tricks him once more by telling Sheldon his grandmother had died shortly before the convention and prevails. It is revealed that this ruse was a scam to win and upon losing, Sheldon tenses up and screams angrily, "WHEATON!" just as James T. Kirk yelled "Khan!!"
Wil Wheaton reappears in the episode "The Wheaton Recurrence" where he has two bowling matches against the main characters. He replaces Albino Bob as a member in Stuart's bowling team. In the second match, Sheldon names his team 'The Wesley Crushers', thinking it a clever pun implying that they will crush Wesley Crusher, who was Wheaton's character in Star Trek. However most interpret the name meaning the team are Wesley Crusher's fans. Wheaton breaks up Leonard and Penny's relationship in order to win a bowling competition, as Leonard and Penny were already having issues because of Leonard's premature "I love you". Sheldon, Leonard, Raj and Howard dress as super-heroines and super-villainesses and go to the comic book store for losing the match.
Wheaton appears again on "The 21-Second Excitation", Sheldon and his friends get in a long line to enter the cinema, then Wheaton comes with Lonely Larry and Captain Sweatpants and enters the cinema without doing the line because of his celebrity status, causing Sheldon and friends to not be able to enter the movies. Sheldon then steals the movie from the projection booth and the gang gets chased by him and the movie goers.
In "The Russian Rocket Reaction", Wheaton invites Leonard and Sheldon to a party at his house. Leonard intends to go with Raj and Howard (until he tells everyone that he got offered to go into space), leaving Sheldon feeling betrayed. However, he has a change of heart when he finds out that Brent "Data" Spiner will be attending. At the party, Wheaton gives Sheldon the gift that he had always been waiting for, a signed, mint-condition Wesley Crusher action figure, saying, "To Sheldon, sorry it took so long. Your friend, Wil Wheaton." Sheldon immediately forgives him and gives him a hug. However, Brent Spiner comes along and sees the action figure. He opens it. Sheldon then announces that Spiner is now his mortal enemy instead of Wheaton.
Wil Wheaton appeared again in "The Stag Convergence" as a guest at Howard's bachelor party. He almost ruins (albeit inadvertently) Howard and Bernadette's relationship when he records Raj's drunken toast (which reveals embarrassing details of Howard's sordid sexual past) and posts it on YouTube, where it's viewed by Bernadette. She nearly calls off the wedding until Howard makes an emotional plea, saying that he's no longer that person and that it's all because of her, and she forgives him (even though she's still mad at him for not telling her about his past).
In the episode "The Habitation Configuration", we see the front of Wil Wheaton's fictional home. The house number is 1701 which is an obvious reference to his time spent on Star Trek: the Next Generation with the USS Enterprise's registry number being NCC-1701-D. Wil agrees to appear on a Star Trek episode of "Sheldon Cooper presents Fun with Flags". Amy is filming it and gets into an argument with Sheldon. Confused he takes Wil's side which makes Amy mad. After getting drunk, he shows up at Wil's house to defend Amy's honor and Wil apologizes.
When Penny has trouble getting her acting career started, she and Leonard consult Wil. He warns them about how depressing it can be to take on projects one knows will be bad (repeatedly correcting Penny when she thinks he is referencing Star Trek). He ends up in a malaise, but is snapped out of it when he finds himself in the TV-guide crossword. Later, after Penny accepts the part in Serial Ape-ist 2, she is surprised to discover Wil is also working on the film, as a mad orangutan (in a full body suit, so as not to be identifiable). Wil seems excited by this development.
Wil Wheaton is also playing Penny's boyfriend in the movie and the scientist who impregnated Penny with the killer gorilla DNA that is slowly transforming her. When Penny asks for another take and the director refuses, they both get fired. While commiserating at a bar, Wil tells Penny that is the craft and art that should be important to her and not some terrible movie. He then gets an audition call for another potentially bad movie and leaves them.
Wil and Penny set up a podcast to talk about their movie Serial Ape-ist 2, with Leonard joining them in her apartment with them as they talk. Eventually actor/director Kevin Smith calls and offers Penny a role in his next movie, Clerks 3. While Penny is interested in going back to acting (a job she had previously shelved to be a pharmaceutical salesperson) Leonard is concerned she will just be disappointed. Wil takes delight in watching them argue, deliberately keeping them on the air. When the two resolve for Penny to take a shot at the role, Wil points out to a dubious Leonard that Penny tricked him into agreeing to let her try out.
In "The Spock Resonance", Wil introduces Adam Nimoy to Sheldon. Adam conducts an interview with Sheldon about what the work of his father, Leonard Nimoy, as Spock mint to him. Showing off one of his prized possessions, the napkin upon which Leonard Nimoy wiped his mouth, and was a Christmas present to him by Penny in season 2, "The Bath Item Gift Hypothesis", Sheldon also showed off the engagement ring that he intended to give Amy.
In "The Opening Night Excitation", when Sheldon decided to spend the evening with Amy on her birthday instead, Wil is the recipient of Sheldon's Star Wars movie tickets. He shows up to the movie dressed as Mr. Spock and enjoys the hatred from the Star Wars fans. While trying to root for the home team since he was in Star Trek, he also wants everyone to realize that it is just a movie. The guys seem to realize that even though they are going to see it again the next day.
In "The Celebration Experimentation", Wil attends Sheldon's birthday party. In his toast, Wil admits that they have had their ups and downs, and even though they met because he was a fan of Star Trek, Wil was a fan of Sheldon Cooper. Also Wil's life has been more interesting because of Sheldon.
- Wil Wheaton did a really good voice impression of Jar Jar Binks from Star Wars, after Sheldon referred him to that character when they meet again whilst waiting to go into the Movie Theater.