Author's Note: While there is an option to import choices from Seasons 1 and 2, because of an error I was not able to so I was forced to create a new backstory. What differences this will make for people reading these solutions, I can't say. None of the achievements are missable and you'll get them anyway, but your experience may differ somewhat from mine. I'll keep these solutions as general as possible to account for that.
Chapter 5 begins with Javi and Clementine in lockup after Eli was shot by Clementine. The closest thing Prescott has to a doctor soon arrives and Javi can either play it cool or turn on the charm ...either way he strikes out. Tripp, the leader of Prescott, shows up and says he'll take Javi and Clem to the junkyard in the morning. Eleanor, the medic, offers to let the two of you out the back gate instead. You're faced with a major choice: leave with Tripp in the morning (Clem's suggestion and what I chose) or leave with Eleanor that night.
At this point, you'll experience a flashback through Clem's eyes that will differ depending on who she ended up with at the end of Season 2. Regardless of your past decisions and the scene you get, the chapter after the flashback concludes.