1. You get a bad end CG and the game takes you to the title screen. You can get the same bad end CG from just dying at the "second phase" of the boss fight (the one on one map) afaik, or at least a way to get it even with the soul girl in your party, so you don't have to intentionally remove it or anything. I got it on my first playthrough but on my second playthrough (which is the save i uploaded somewhere on this thread) I forgot to lose intentionally to get it... so in that sense I suppose it's missable.
2. If just handing in doesn't work, what version are you playing? I believe if you're at v2 or more recent, just save and reload. You should get a selection when you start, asking if you want to progress to v2 story or no. progressing v2 should net you the bounty... though it's been a while since I cleared the story mode so I may be recalling things incorrectly.
3. There's more to the game after it if you're on v2 or more recent version.