The center of the story of the second episode of 'Big Bang Theory' Season 9 is about the relationship problems being faced by these two couples -- Leonard and Penny, and Amy and Sheldon.
According to Vine Report, the relationship of Leonard and Penny is on the verge of breaking up, because Penny found out that Leonard had a short fling with Mandy Chou in Episode 1. Penny attempts many times to talk to Leonard to discuss their relationship problems, but the latter avoids it every time.
When Penny tells Amy and Bernadette about her problems with Leonard, Amy suggests that she set aside her anger for the time being.
Leonard and Penny eventually reconcile and both of them acknowledge that their insecurities have been the cause of the problem.
On the other hand, the problems between Amy and Sheldon continue to worsen after Amy refused to film Sheldon's latest "Fun with Flags'' episode with him. So Sheldon records the episode alone.
The first episode of 'Big Bang Theory' Season 9 focused on one couple's continued break-up (Sheldon and Amy), and another's attempts to fix their relationship problems (Penny and Leonard).
The reason for the latter on why they look so miserable may be due to the fact that their marriage appeared to be so short.
The storyline allowed Penny and Leonard to question whether their relationship problems were really down to their worry of each other leaving for a more suitable partner.
Digital Spy reported that Leonard was seen in the funniest scene having a nightmare involving Sheldon coming up with a way for Penny to seek revenge on his naughty kiss -- by passionately kissing him.
There was certainly an improvement in this week's episode as compared to last week (not too hard a task after the dour opener). It is assumed that the main focus of this season will revolve around Sheldon and Amy's split, and Leonard's marriage issues will be put on hold for the time being.