Seems like they're preparing a new part of Time Temple.

Has the black Mage actually done anything considered "ultimately evil"?
I mean, he caused big bang, but that was arguably a good thing.
Future henyses/ereve scenario, he didn't do anything, the Cygnus empress did.
Back during the time of the "Legends", is it even established why they're fighting him in the first place?
All he's doing is chilling in present door ToT not bothering anyone
Nexons just pinning all their game changes on him.
"OMG BIG BANG BLACK MAGE DID IT"
"OMG CHAOS BLACK MAGE DID IT"
In fact, he's never done ANYTHING I'd classify as evil, correct me I'm wrong.
LEAVE THE BLACK MAGE ALOOONE

So you're just going to ignore the fact that he set a trap that turned Cygnus evil in the first place?
Or are you pretending that that was a benevolent action?

Pretty sure it was established that he was trying to conquer the whole damn world. You know, that generic stuff.
Still good enough reason to stop him.

If nothing else, he ordered for Slayer's house to be burned down, so he killed at least two innocent people there.