>>716250603You have to complete a few of the repeat missions. They're there as stand-ins for the Kingdom of the Fly missions that were cut earlier on.
>>716251068That's not quite it, you just have to get her above a certain level.
The butterfly thing was that originally, you could put the emblem on to prevent her from leaving, but then you could never finish the game because she's supposed to leave.
Originally on release, the intent was that she leaves and then she's gone forever, and people bitched so hard about it that much later on when Konami took control they patched it so that you can use it to get her back after she leaves in the story, because people were just hacking her back in anyways.
An upgraded D-Walker is supposed to overlap with her somewhat but people thought it was lame.
The current version of TPP is somewhat different from how it was on release.