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Pain and Obito is leading the Akatsuki in search for a Jinchūriki who's hidding in Berlin. The Avengers are called and several imprisoned members are released from the prison to stop the Akatsuki from destroying the city.

The Avengers
Thor
Vision
Hulk
Ironman
War Machine
Scarlet Witch
Ant Man
Spiderman (Composite)
Falcon
Helicarrier boarded with Nick Fury and other SHIELD personel
Quinjets operated by Black Widow, Hawkeye, Cap, Bucky, Panther

VS

Akatsuki
Six Path of Pain
Tobi
Konan
Itachi
Kisame
Hidan
Kakuzu
Orochimaru
Deidara
Sasori
Demonic Statue of Outer Path

Round 1: Random encounter

Round 2: The Avengers have knowledge about them.

Which team wins and why?

Avengers

Wrong forum. But Akatsuki should stomp.

It's almost like the OP just loves seeing Naruto characters stomp comic book characters.

But yeah, pretty much every single person on the Naruto side has a hilarious speed advantage, some of them have wacky mental powers the other team has no defense for, as well as other just wacky esoteric powers the other team has no defense for.

Itachi can put you in some weird mental dimension, has magic black fire that can't even be put out by normal means, and that is just one guy and not even the most powerful.

Itachi also has Susanoo. A gigantic energy armor that is basically invulnerable and has massive and powerful aoe2 attacks.

Not to mention that they also summon their animal friends like Orochimaru's giant snake.

I'm tempted to say some of the Akatsuki are strong enough to maybe solo the Avengers.

Akatsuki wreck here.