The second episode opens with an extensive recapping of the pilot. Sarah is now working undercover serving hot dogs next door to the Buy More. The agents bring in the doctor who designed the program trapped in Chuck's brain. The doctor says that he can remove the program from Chuck's head but when the doctor leaves his car blows up. "The old exploding cell phone". The agents accuse each other for the murder. The data in Chuck's brain tells him that the exploding phone is an NSA weapon. There is a great fight sequence set in between the two agents at the hot dog place. It turns out that the Doctor faked his death in order to kidnap Chuck and sell him to Korean interests. While flying off in a helicopter Chuck accidentally shoot the pilot with a tranquilizing dart. The big finale involves Sarah having to talk Chuck through landing the chopper by having him recall flight simulator games.
I still stand by my first impression that the premise will burn out real fast and Zachary Levi is not a good fit for this show.
To quote Chuck (to himself), "Don't freak out".