They are Ontos' pure logic without neither of Alvis' humanity or the other Aegises' moderating factors. Their plan is to destroy Aionos and create a new world which only includes the City's denizens. As this runs counter to the agenda of both the Liberators (restoring the worlds by resuming the Origin process) and Moebius (preserve the status quo) and due to how dangerous Alpha is (Their first shown act is to effortlessly defeat Shulk and Rex, severely injuring them in the process), both groups are in a truce while they deal with Alpha.

They spend most of the game commandeering Na'el (Xenoblade)'s body due to her own anger against Aionos and the warring nations. This is how N (and consequently M) even originally came into being as Moebius, as a counter to Na'el's emotions. Them encountering N and Ghondor blowing himself up is the event in which the repressed Alvis personality split from them, becoming A.