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I think I mentioned this in another thread similar...

My entrant would be the Zentraedi from Macross/Robotech. Militarily they'd destroy the Imperium on sheer weight of numbers (and a Regult Pod is some 60' tall and they have...billions of them). Their fleet is massive and they seem to care little for losses. They have ample planet-killing capability and seemingly decent FTL travel. Their Robotech factories are absurdly massive and produce more war materials than anything in the Warhammer universe.

However, if we believe the cartoon and singing or emotion is so unsettling that they can't do anything or they fail to act...then even the most meager psyker from the Warhammer universe could (in theory) stop an entire fleet.

So, militarily...90% Zentraedi win.

Introduce psykers...100% Warhammer win.

Along Sci-Fi lines, not sure if you consider it an Advanced Species.

but IoM Vs Rick Sanchez.