A mysterious group of ninjas makes a surprise attack on the Konohagakure, which takes great damage. The nightmare of another Shinobi World War could become a reality. Sasuke, who was still a missing nin from Konoha trying to kill his brother, Itachi, appears for the second time in front of Naruto at an unknown location to prevent it from happening.

X-Men, still grieving over the death of Phoenix (Jean Grey), are investigating a case of a missing mutant girl in Northern Japan. This leads them to a mysterious virus that turns mutants into monsters. U-Men and the Inner Circle want it.

Assigned on a mission to capture Mukade, a missing-nin, Naruto Uzumaki sets out for the once glorious historic ruins of "Ouran", where he pursues and corners the rouge ninja. Mukade's goal is revealed to be a dormant leyline within the ruins; he unleashes the power of the leyline, causing a light to envelop Naruto, sending him into the past, 20 years before the series began. When Naruto awakens, he comes into contact with the Fourth Hokage, Minato Namikaze.

A terrorist group invades a laboratory containing a deadly bacteria and destroys the lab with an explosion. They later announce via the internet they have gained possession of the bacteria and declare themselves to be the Red Siamese Cats, a terrorist group that was eradicated a decade ago.