According to Steve Holland who is the show-runner starting with this season, Wil Wheaton will return in this season since his absence from Season 10. And this has confirmed to be true since it has been stated that he reappeared in "The Proton Regeneration" (S11E6), along with Professor Proton, their first appearances since "The Opening Night Excitation" (S9E11) and "The Celebration Experimentation", respectively and a span of 43 episodes and a span of 37 episodes, respectively. Wil also returned in the 15th episode. Wil will also return for Sheldon and Amy's Wedding.
Sheldon and Amy are surprised to find that Wil Wheaton's new Professor Proton show is actually very entertaining and that Wil had Howard on as a guest. On Howard's suggestion, Sheldon apologizes to Wil, mending their friendship, and tells him he wants to be on the show; but Wil asks for Amy. Sheldon tells her to do it, but she says she often doesn't do things to avoid upsetting him. Sheldon is horrified when he realises how selfish he has been, especially when he finds out that the men do the same for him. Sheldon encourages Amy to go on the show to inspire girls to pursue science while trying to control his obvious jealousy for her. Meanwhile, Leonard writes a book about a physicist that solves a murder, the protagonist Logan Dean is based on himself. Bernadette points out Logan's mean boss Illsa is similar to Penny, who thinks it is based on Bernadette, though Leonard does not correct her. However, Bernadette tells Penny the truth, upsetting her and making her mad at Leonard. After calling his mother for advice, Leonard learns that Illsa is actually like her; but abandons the book when he realizes he wrote romantic tension into the relationship between the characters.
Mayim Bialik as Amy Farrah Fowler (guest star season 3, starring seasons 4–12): A woman selected by an online dating site as Sheldon's perfect mate. Amy is from Glendale, CA. While she and Sheldon initially share social cluelessness, after befriending Penny and Bernadette she eventually becomes more interested in social and romantic interaction. Her relationship with Sheldon slowly progresses to the point at which Sheldon considers her his girlfriend, eventually they get married. Amy believes she and Penny are best friends, a sentiment that Penny does not initially share. Amy has a Ph.D. in neurobiology.
Amy enthusiastically accepts Sheldon's marriage proposal. However, when dining with Amy's colleagues later that night, Sheldon is offended that they are more impressed with Amy's work than his own. With help from Stephen Hawking, Sheldon later comes to grips with the fact that he will not always be the center of attention in the marriage. Bernadette is shocked to realize that she is pregnant again. She and Howard are not thrilled at the idea of having another baby so soon after their first. They attempt to convince Leonard and Penny to have a child as well, but are rebuffed.
Howard dresses as Sheldon for Halloween at work, hurting Sheldon's feelings. When Howard does not apologize, Amy and Sheldon dress as Bernadette and Howard at Penny and Leonard's party, angering Bernadette. Sheldon and Bernadette later bond over their painful childhood memories. Leonard is upset that Penny does not seem to remember that their first kiss was on Halloween. Penny later admits she does remember, but does not like to think of their first kiss as an unromantic drunken hookup. She likes to imagine their first kiss was one they shared on Leonard's birthday, which pleases him.
Sheldon and Amy go on their honeymoon to New York City, starting with Legoland New York. Sheldon's insistence on scheduling their marital relations stresses Amy. He says he only does it to remind himself to be intimate with her. They compromise by letting him make a schedule without sharing it with her. Leonard and Penny discover Mr. Larry Fowler (Teller) in Sheldon and Amy's apartment hiding from his wife (Kathy Bates). Leonard notices parallels in his own marriage, which offends Penny. Leonard apologizes, and Penny convinces Mrs. Fowler to give her husband a break. When Mrs. Fowler wants to hang out with her regularly, Penny scares Larry out of the building. Raj instigates a Twitter feud with Neil deGrasse Tyson but is scared off when confronted over the phone. Neil then calls Bill Nye to scare him, too.
Sheldon is annoyed that Amy does not have time to work on the super-asymmetry project with him so he talks President Siebert into getting her removed from her own project at the university. Amy is angry at both of them as she wants to still have her own identity outside the marriage. When confronted by Amy, Siebert apologizes to her but states that it will be difficult for the university to give her her project back. After talking with Arthur Jeffries in a dream, Sheldon apologizes to Amy and both of them talk about their fears in their marriage. Meanwhile, Raj does not want to have Howard join him in his show at the planetarium, thinking he'd just use his astronaut status to make it about himself. Raj eventually lets him join in and Raj and Howard spend the whole time complimenting each other, surprising Bernadette, Leonard and Penny.
I read through the article and all the comments (which makes me miss TBBT even more and it hasn’t been off the air a week yet) and noticed that 3 of my favs aren’t mentioned. (1) episode where a bully (Todd Sornecki) steals Sheldon’s online trophies and Penny kicks him in the nuts for Sheldon; (2) the episode where they reveals each others secrets (Leonard slept with Priya; Raj used Sheldon’s tooth brush; Howard told Raj foreigner give gifts to Americans for certain holidays and Sheldon put moths in Leonards food “for science”; (3) the episode where Amy and Sheldon go to the aquarium “as friends”, when Sheldon tells Amy “I can handle a lot of things Amy but getting over you isn’t one of them, I think we should just be friends” it breaks my heart everytime; (4) the episode where Priya buys Leonard glass and he walks into the cafeteria and causes mass chaos, that’s a classic; (5) the episode where Priya ruins the roommate agreement between Sheldon and Leonard, when Leonard buys Sheldon Greek food it’s hilarious. Sheldon gets back at Leonard & Priya by threatening to send an email to Priya’s parents telling that “she’s in a relationship with the whiter than marsmellow fluff Leonard Hofstedter”. Ok just one more, when they all take a road trip to speak at the science convention and Bernadette runs into her former professor/lover played by Rick Foxx and Sheldon banished Penny to the “love car” and Bernie and Howard sing Sonny & Cher “I got you Babe” is funnier than hell. I still crack up when I see Raj look down at Howard’s junk to measure Howard’s junk against Rick Foxx’s, I can’t believe the sensors let that through.
The show originally centered on five characters living in Pasadena, California: Leonard Hofstadter and Sheldon Cooper, both physicists at Caltech, who share an apartment; Penny, a waitress and aspiring actress who lives across the hall; and Leonard and Sheldon's similarly geeky and socially awkward friends and co-workers, aerospace engineer Howard Wolowitz and astrophysicist Raj Koothrappali. Over time, supporting characters were promoted to starring roles, including neuroscientist Amy Farrah Fowler, microbiologist Bernadette Rostenkowski, physicist Leslie Winkle and comic book store owner Stuart Bloom.
When Mayim Bialik first learned she had to say goodbye to neurobiologist Amy Farrah Fowler, she opened up about the show ending in a blog post, asking, "And now I start to figure out what next. Where will life take me? Where will this career go? What do I want?" Up next she has a voice role in The Inspector Chronicles, a quasi-parody of Doctor Who making the leap from short to feature film. She'll reprise her role as the voice of the Inspector's time machine, known as B.O.O.T.H. Aside from that, she doesn't have any major projects lined up, aside from preparing to not see her close-knit cast the way she'd grown accustomed to. "We'll have to see what our lives look like," she told Us Weekly in early May about the chance they'll remain close. "I mean, we're all going to be on different schedules now; it's very different."