Okay here is the plot this takes place after ultimate alien but before omniverse Ben has the new omnitrix but the new omnitrix has the evolutionary function unlike canon.
So Ben ends up in the warhammer 40k universe how he ends up there is up to you but he ends up somewhere in the imperium of man.
Ben is recruited by an open minded female inquisitor who wants to use him against the imperium's enemies and that is the ONLY reason why the imperium is allowing him to live.
The imperium hates Ben because he is a heretic because he doesn't worship the emperor and worst of all uses xeno technology which is also a crime in their eyes.
So even when Ben's working for the inquisitor other imperials will send assassins after Ben and he will have to fight to survive.
The story is to show Ben's emotional and mental struggles in the 40k universe as he is forced to discard his morals to survive and as he is hated by everyone including the very people he saves.
He is hated by the imperium he serves, he is hated by the imperial citizens and soldiers he saves.
Ben is allowed to have a few friends though such as a sanctioned psyker and/or an abhuman who are also treated as outcast by the imperium.
Ben's omnitrix must acquire the dna of warhammer 40k aliens and give them ultimate forms (it wouldn't be the omnitrix if it didn't acquire the dna of new aliens)
The pairing is Ben x female inquisitor (the female inquisitor must be an oc of yours)
So Ben must serve the imperium he must serve a female inquisitor to be exact.
How he ends up in her service is up to you but being in her service is the ONLY reason why the imperium is allowing him to live and even then they'll try to look for every reason they can think of to execute him for heresy.
And other factions will be after Ben as well
The chaos gods, Like with every other mortal with great power, they would think that Ben would be a fun pawn to play around with Thus, if they're not trying to corrupt him, then they're throwing their champions at him just for the sheer heck of it
And the servants of Chaos would in turn come after Ben with everything they have to try and kill him.
The reasons may vary a bit.
Some may do it to gain hold of the omnitrix, others to gain favor with their Dark Gods (followers of Khorne most of the time in this case), while some fear that Ben could grow to be a potential rival in the Great Game
The dark eldar will want to gain hold of the omnitrix and try to steal it from Ben.
The orks will probably enjoy fighting Ben and some warboss might try to steal his omnitrix as well.
Anyways if you want to write this say so in a review or contact me!