Play any first person shooter, and start attacking a large group of enemies. What happens? That's right, they start shooting you in return. They don't just stand there thinking it's time to be a hostage. This is basic fight or flight response. They were armed and were ready to attack, that's where you made your mistake. He's doing what would have happened realistically given the situation, and you're expecting X and his buddies to be the invincible heroes yet again after exerting deadly force in a fragile standoff situation. Sorry, but no.
Also, the UN wouldn't have allowed Galactic Plasma to come Mossdeep either. The place was initially supposed to be empty and not be in operation, I thought we agreed on that, hence why Chan gave Alex the access card anyway. If Black Alpha didn't attack, would you still have sent UN operatives to intercept Galactic Plasma when they trespassed into UN territory? You would have had to, because it wouldn't have made any sense otherwise.
And lastly, yes, I decided to give Requiem a boost in power because I figured Black Alpha badly needed it, and I was glad he stepped up to the plate to help that side of the story out. And then you jumped in with the expectation of ruining all that, and saying "see you in February" like this was some kind of joke or something. Really, man, how do you expect me to bunny your character for almost a month and a half after doing something like this? Point is, I wouldn't. I'd retire him from the RP one way or another. And I must ask, could you really blame me?
Really though, how do you think this should be resolved? Pretend this is a fan fiction and you get to write what happens next.