Really? I thought this just happened on the 616. We haven’t seen all of Nate and Dani’s relationship, so maybe this scene is a little bit before Dead Souls but still far enough that Nate has known he was dying for a little while. The earlier iteration does make sense, too. It also makes sense that Nate would send Dani away, maybe she’s even a construct who saw what Nate was doing to the real X-Men and tried to stop him before X-Man did a major mindwipe and plucked her in jail.
He wasn’t acting like a moustache twirling villain, though. He saw that things were really shitty for mutants in the 616 and, probably through a little psychic brainwashing, found that this world was probably the best place for mutants to be. He’s no Spurrier!Legion but he’s at least been consistent with how it’s been with Disassembled. Plus, we know that a part of him already doesn’t agree and has been helping the main cast.
He’s just a tough parent with very, very tough love. Without him, Cable and the mutant messiah would’ve died to a dear. Kind of embarrassing.