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As the title reads. The fight is in the city from Teen Titans. No early knowledge of each other. Two rounds:

1. No Master Control on Omnitrix
2. Master Control is on.

Who wins and why?

Even without master control Ben can just go Atomix or NRG and wreck them. Or Whampire and control their minds. That's not all, just one of the best options. And they're nothing he hasn't faced before.

Well, Cyborg is immune to mind control, so there is one flaw to what you said. As for the others, I have not seen Omniverse yet, so I'm not sure who any of those aliens are or what they can do.

Both manipulate radiation and nuclear/atomic energy. And Atomix can literally set off a nuke. Or he could just go Alien X since Bellicus and Serena have given Ben full control over Alien X so they can continue to argue for all eternity.

Well, I may have to bar Alien X, since he is a little too cheap for this fight.

He still has plenty which can help. He could go Upgrade and turn Cyborg against the team and they wouldn't hit him since hes still Cyborg. Or he could go Clockwork and freeze them in time.

Also he's got Skurd now who can give him boosts like giving him Diamondhead armor and weapons while Ben is Four Arms.