Square Enix's Marvel Avengers game will tell an original story. During the reveal of the game at E3, voice actor Travis Willingham, who'll play Thor in the game, confirmed that the game is not directly based on a classic comicbook story.
Willingham, who also voices Thor in the Avenger's Assemble cartoon (and will star alongside Nolan North and Troy Baker in the game) says that "having an original story to tell, as well…what they've done at Crystal Dynamics is great, so I think everybody's going to be preeeetty stoked." That confirms that the game's narrative is a new creation, rather than something based on a previous Marvel story.
While that's not hugely surprising, it is a marked change from the Marvel Cinematic Universe. While some of those stories have been their own, several of them, including Captain America: Civil War and Avengers: Infinity War are drawn directly from the original comic books before being adapted for the big screen.
It's probably, however, a little easier to adapt a story from book to film than it is to turn it into a fully fledged co-op game in which your players take direct control of the characters. It's yet to be confirmed precisely why Crystal Dynamics wants to tell its own story, but I'd wager that'd be part of it.
You can check out Willingham's comments for yourself in the video below:
https://youtu.be/19czaASklAs
More information about the new game is likely to come out over the next few days, but we've got a decent amount to be going on with now, including a new heroes will arrive in the game at no extra cost. Given how long we've been waiting, it's nice to have so much to go on.