I kinda see the characters in boss fights as a sort of justice League type of thing where they take down interdimesional threats and villains. They have like a central meeting place and inky, collector, eggy, and the other big names are the leaders (though collector is the main guy).
Anyway basically, if it's like, a villain or smth and they are defeated but don't die they get their abilities taken away and then put into a prison (maybe kinda like SCP stuff yk).
Interrogations sometimes occur, and 401 is very useful for this because she's very intimidating and is fine with scaring someone shitless