Here, I got this.
AF and UA retconned Kevin from a mutant to an alien hybrid, along with pretty much changing every superhero thing about Ben 10's earth to being aliens. A big goal of Omniverse was to change as much of that back to the OS's "aliens are a thing but earth has other superhero shit going on too." standard as they could.
The Rooters were a big spy story because the Plumbers were originally a secret organization instead of space cops, with the Rooters being revealed to be the hard line remnants of that refitted into a black ops unit.
It was revealed that the Rooter leader used Kevin's powers to transfer alien DNA to the "Plumber's Helpers", kids who were introduced in AF as alien hybrids. These kids were brainwashed and trained as soldiers for the sole purpose of getting close to and killing "the coming storm", Ben 10, who the Rooter leader believed was too wild and immature to handle the power of the Omnitrix; and, indeed, that no one should have it and that it should be destroyed, making him almost unique among Ben's rogues.
Anyway it's revealed that Kevin was a willing partner with Cervantis (the Rooter leader), having his memory edited to get close to Ben when an inital direct attack on him failed. Kevin later got his memory back, and furthermore his unique mutant brain chemistry makes him resistant to Cervantis's telepathy; he essentially faked being won over by Cervantis in order to position himself and Ben to take him out and free the kids of his psychic control.
It's later revealed that future Kevin ends up leading a reformed Rooters unit.
tldr; Kevin's a mutant again, and was working with Plumber black ops to kill Ben aided by a psychic who messed with everyone's memories to cover his tracks, but actually reformed and cleaned house of the old guard who wanted Ben dead.