I think you can tell why none of them are responding to the GF anymore.
I’m going to do my best to never let it cause a problem, but essentially, you get ten normal seconds of Hypermode once that cutscene plays. After that, your Hypermode gets “corrupted” and the Phazon starts filling instead of staying at a steady level, and you can’t cancel Hypermode. Normally, canceling Hypermode early gives back all the energy you didn’t spend. However, if you let the red bar fill all the way back up, it’s an instant game over. It gives a special cutscene, so hey, that’s cool. But I’ve never actually experienced it because it’s so easy to prevent. Rather, if I’ve spent a lot of energy and still have foes to confront, I might just sit in Hypermode for a bit so I can get some free ammo.
It’s fairly obvious that what happened to the others is that they let the corrupted Hypermode bar fill up, not knowing what it would do. When that happened, they became Phazon-fueled villains. They obviously didn’t join the Space Pirates; I think they just killed everything that moved. Rundas didn’t attack Samus the first time they met back up probably just because it was a really poor arena. He needs more space to get to work.