Until this episode, Alphas only had Alpha-related cases. "Bill And Gary's Excellent Adventure" has no hint of an alpha doing something bad and instead is about a fairly run-of-the-mill kidnapping and ransom. It makes sense that there would be an episode that resolves Bill's ties to the non-alpha law enforcement establishment. Bill, with Gary in tow, solves the case and gets an offer to be reinstated into the FBI, something he's pushed for and brought up many times, but he declines the offer and stays with the team. The team is clicking and Bill has people around him with similar problems. This is what Dr. Rosen wanted all along and Bill has legitimate reasons to stay.
The other plot development was Nina and Hicks almost hooking up. They don't follow through because Nina interrupts, but it was clear where they were going. One of the big things we learn is that Nina killed her ex-boyfriend by pushing him to kill himself. While the writers make it perfectly clear that the boyfriend was no good person (though I thought the bit at the end about the financial scam was a bit much), Nina is scared of what her powers can do coupled with her emotions. It's a deadly combination and she doesn't want to repeat mistakes of the past.
I know some people may hate him, but Gary is my favorite character. Although his behavior may be annoying at times, the writers give him so many funny throwaway lines that I think he's great, and Bill plays off of him nicely.
Next week, Summer Glau! Cue the collective nerdgasm.