[quote=@Zyx]
<Snipped quote by Sep>

>I see. Well I assume the real heavy-hitters like Xeeleeverse stuff, Doctor Who (mostly Gallifreyan or other High Evolutionary/time active civ tech), and Manifold (mostly Downstreamer related ships) are strictly off-limits given how trivial a lot of them would make the Replicators threatwise. Could something on the scale of certain Forerunner or even Culture ships and the like work? Or would those also be too much?
[/quote]

Forerunner I could deal with I don't know anything about Culture. Its important to note Replicators want to integrate more powerful technology so the higher tech the bigger target you put on your back.

[quote=@Dead Cruiser]
This is a fun concept. I have a few ideas.

Horus Lupercal, commanding the Vengeful Spirit, or if a more benevolent character is desired I would sub in Sanguinius, commanding the Red Tear. 
[/quote]

I mean the thing you need to remember is these characters have been chosen as a benevolent being thinks they'd do the job well.

Now can characters have alternative agendas? Yes.