The legend claims that Arthur will return from Avalon at the time of England's greatest need, which frequently gets interpreted as "at the end of time." (I have a sneaking suspicion that Anti-Christ is going to try to pass himself off as Arthur returned, among his "fulfilling" other legends--but that's JMO.) I can't remember offhand when "Men of Legend" is set SPN-wise, but if someone is trying to restart the Apocalypse--maybe Raphael, maybe Abaddon, maybe Casifer, or maybe just some wacko doomsday cult [ETA: ooh, or Rowena!]--bringing Arthur and Merlin back might be one of the methods tried. However, since there's already been one connection between SPN-verse and Merlin-verse, maybe the spell goes astray... or maybe Arthur wasn't real in SPN-verse, or was killed in Season 4 as one of the seals or something, so the spell grabs the next available versions, which are the Arthur and Merlin from Merlin-verse. *shrug*

I look forward to reading whatever you do come up with next!