One of the advantages of a long-running video game series is the player can grow attached to the characters over time; after all, fans are still buying Sonic games despite the series producing nothing but junk for at least a decade.
So while a series will likely stick to a familiar formula for both story and gameplay, some of them still like to break the rules and toy with players emotions now and again. Beloved characters can be killed off (RIP Eli Vance) and the heroes can really be put through the emotional wringer; and if the game’s creators really want to mess with you, they’ll turn a hero into a villain too.
If this switch is done right it can be unexpectedly emotional, having to deal with a character you’ve grown to like suddenly turning to the dark side. In a couple of instances, they weren’t all that well defined to start with, so the twist doesn’t have the impact it was supposed to; when it works, though, it can hit you right in the feels.