So there are a few things that might be spoilers if you haven't finished the game yet, so I'll answer as spoiler free first and then spoilers afterward.
When Chase condemns Flynn don't forget that you were only given the one choice to condemn Flynn. This occurs no matter what previous choices you made on the route and it stands out. Keep also in mind the weird moment previously where Chase was hiding in the bathroom and the point of view shifted. As for Chase being a manipulative bastard/having a moment... People like to argue about that. My stance is Chase wasn't really himself at that moment, but I understand why people would think he is a manipulative bastard.
SPOILERS
It is sort of revealed throughout Flynn's route, but heavily explained in Jenna's route, that Chase was possessed by a spirit that is sort of Sam from The Smoke Room (I say sort of cause it gets complicated what exactly it is). Jenna's route further explains that whenever Chase is indecisive (Which he frequently is) Sam would step in and make the choice for him (with us essentially acting as Sam by making the choice). This also means that the choices presented are not fully Chase's but options given to him by Sam/the Player. What Chase does after a choice is made is somewhat his own actions, but its hard to say how much of Chase's actions are really his own due to the possession.