Bernadette's due date arrives but she still hasn't given birth. As Amy and Howard work together at the college, the rest of the friends try various ways to initiate her labor, though Sheldon wants to play a complicated board game instead. Amy shocks Howard by saying Bernadette has already decided to name the baby after her father, Michael. He doesn't agree and everyone makes suggestions as to what to name the baby. Bernadette goes into labor and gives birth to a son named Neil, after Neil Armstrong, Neil Gaiman, and Neil Diamond, with Michael as the middle name. At the last minute, Howard relents to name him Michael as Bernadette got six stitches.
Two months after the events of "The Change Constant", Sheldon and Leonard repair Sheldon's DNA molecule model as everyone prepares to fly to Sweden for the Nobel Prize award ceremony. Howard and Bernadette nervously leave their kids for the first time with Stuart and Denise, while Raj leaves his dog with Bert. Penny has become pregnant, though she and Leonard are keeping it a secret. On the flight, Raj thinks he spots Sarah Michelle Gellar. Penny's frequent bathroom trips make Sheldon fear she is sick. Leonard reveals the pregnancy to Sheldon, but instead of being excited for Penny, Sheldon is only selfishly relieved that he will not get sick and he exposes the pregnancy, offending Leonard. At the hotel, a series of minor incidents with their kids make Howard and Bernadette want to go home. Much to their dismay, Sheldon is still insensitive. Amy furiously tells Sheldon he broke their friends' hearts and they only tolerate him because he does not intentionally do so, which she also sometimes does. Everyone decides to stay for the ceremony and Raj brings Gellar. After they are awarded their medals, Amy encourages girls to pursue science while Sheldon thanks his family and then individually acknowledges each of his friends and Amy as his other family who always support him. The episode closes with the gang eating in Apartment 4A (an allusion to the final scene in the opening credits) as an acoustic version of the theme song's chorus plays.
After the birth of Michael, Howard and Bernadette are unsure who should stay home with the kids. Howard decides to look after the kids one day to show he has what it takes to care for them. While Bernadette falls back in love with her job on a trip to the office, Howard is quickly tired and realizes he might not have what it takes to be a stay-at-home dad. Howard and Bernadette realize neither them is ready to give up their job.
Sheldon cannot find the perfect wedding date and begins talking in his sleep, adopting the persona of a laid-back person who goes with the flow. Amy and Penny believe that his subconscious mind is trying to tell him to be more relaxed; his attempt to be so while wearing flip-flops ends in disaster. He decides to leave all the wedding planning to Amy while he wears a Star Trek uniform underneath his tuxedo. Meanwhile, Raj and Stuart both become interested in Bernadette's new coworker Ruchi. While she likes them both as friends, she does not want a relationship with anyone.
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Science has also interfered with the characters' romantic lives. Leslie breaks up with Leonard when he sides with Sheldon in his support for string theory rather than loop quantum gravity. When Leonard joins Sheldon, Raj, and Howard on a three-month Arctic research trip, it separates Leonard and Penny at a time when their relationship is budding. When Bernadette takes an interest in Leonard's work, it makes both Penny and Howard envious and results in Howard confronting Leonard, and Penny asking Sheldon to teach her physics. Sheldon and Amy also briefly end their relationship after an argument over which of their fields is superior.
When Leonard receives a braggy Christmas letter from his brother, he feels bad about how little he and Penny have achieved in the past year. Leonard wonders if he and Penny should be thinking about the next step after two years of marriage, like buying a house or having a baby. Penny tells him she wants to do all those things someday, but she has a bunch of stuff she would like to do first.