This discussion may contain spoilers!
I posted this as a reply in another thread, but I feel deserves it's own discussion. The theory operates under the assumptions that:
1) Lily and Kenny survived their disappearances. 2) Tavia's group finds both of them.
Let me know if you think this theory works and/or would make a good episode (or part of one), the likelihood of seeing something like this in game, and if you enjoy reading the theory in general.
Alright guys, if this choice does make it into season 2, what situation do you think would bring it about? Maybe both end up at Tavia's settlement and someone (Bonnie?) gets murdered and Clem has to help decide which of them is responsible because no one would suspect a kid snooping around and they don't want anyone to panic. Most evidence would probably point to Kenny since it would make the decision more difficult on the majority, maybe initially withdrawals appear to have incapacitated Bonnie and someone kills her fearing reanimation. Maybe Lily hates Bonnie (thinks she's weak, a resource drain, finds out Bonnie's group stole from others etc.) Kenny's cap is found nearby (making it look like the Larry in the locker situation for Kenny, but also implicating Lily at the same time). In the end, the person Clem thinks is responsible is sentenced to death. "We're looking for good people," and exiling a murderer could bring about his/her revenge on the community later. So they kill him/her. Of course in the end it will end up being neither of them. Maybe Kenny and she had been hooking up, lonely after losing Katjaa and Duck, and he forgot his hat and her death was perhaps suicide over what she did to Leland's wife? Becca finds out she was one of the 'bandits' that tore her group apart? Angry Leland? but once the truth comes out it will be too late.
Let's assume that it is Becca who kills Bonnie, Becca is then also killed by Tavia's group. This makes Clem feel unsafe, guilty for a friend's death (wrongly accusing Lily/Kenny) and Shel feels betrayed by Tavia so they leave together for the next episode...
In the determinant case that Shel and Becca didn't leave with Tavia, it was a suicide and Clem leaves alone only to run into Shel who has recently lost Becca to walkers, so the next episode starts the same with Shel and Clem together.