They’ve said that they want Halo Wars 2 to have that similar sort of mystery and twists that the first Halo did. If that’s the case, well, in that game the Covenant unwittingly unleash the Flood. So, how could this new Banished faction be doing something or release something that might doom the galaxy.
Firstly, why are they on the Ark? Theres only two things there, the Halo array and Mendicant Bias. Whats the main obstacle to Atriox taking over the galaxy? At the minute its Cortana who controls all of the Forerunner Tech. So, hes obviously on the Ark to get something to help him get rid of Cortana and her Guardians.
Can the Halo array do that? Technically yes. It did destroy the Domain and presumably Atriox would be safe to activate the array from the Ark with his followers. However, this would kill all life in the galaxy and make him Master of Ash. You can’t rule a Galaxy with everyone dead. If Atriox is all about power and not religion he isn’t going to go down that road. Probably. 
Can MB do this? Yes. We don’t exactly know how powerful she is within the Domain, the Warden seemed impressed for whatever that’s worth and shes done enough to conquer two relatively primitive societies. But MB is THE most advanced AI the Forerunners ever built. Logically he would beat Cortana. But, we know that MB (assuming the rest of him feels the same way as that shard) wants to help humanity claim the Mantle. Atriox does not approve of this. But more generally, I can’t imagine the story resolving itself like that. Oh, Atriox frees MB and then MB helps humans. No, if the story is like Halo CE then it has to go south and they release an ancient evil. As I said though, its unlikely to be MB himself.
So what if, Atriox has a very fragmented and warped knowledge of the Ancient war against the Flood. He knows about this thing called the Logic Plague which brought Mendicant Bias, their most powerful AI, down and so thinks it must be a weapon that cripples AI. He doesn’t realise that MB main body is still infected with the Logic Plague or the effects that using this on the Created will have. They could even copy the CE bit with the Chief helping 343 GS and have the humans hijack his plan only to realise that this is a terrible mistake. I mean the Created are monsters, but they’re not helping THE THING eat us and release the Flood. Plus if all those AI go crazy then they really will just start nuking cities and gunning people down in the street with Prometheans. It won’t be nice.