Mizuki gave the demon brat his task and then waited outside the Hokage tower. When the brat departed with the scroll towards the forest, Mizuki followed. Once he reached the clearing he intended to learn the required skill in, Mizuki dropped from the trees and quickly plunged a kunai through the back of the kid's head, killing him instantly.
That done, he grabbed the scroll and left, leaving no trace of his presence to be tracked by.
Everyone would later assume Naruto tried to give the scroll to some contact as a way to spectacularly betray the village, got doublecrossed and the Forbidden Scroll was stolen by some foreign spy. Shame and misery was spread all around for all of those who felt guilty about being the cause of Naruto's betrayal and subsequent death, indirectly.
Mizuki would later kill himself attempting to learn some of the techniques in the scroll.
Iruka would wallow in self pity for years before dying on a routine mission.
The Sandaime abdicated in favor of Danzo, realizing that he was such a poor leader that he couldn't even protect a single boy. He died soon after, officially of natural causes, unofficially assassinated by Orochimaru.
Kakashi returned to ANBU and died soon after.
Jiraiya retired and became a full time porno writer. He died of a liver infection after a long life full of excesses.
Tsunade agreed to lend her expertise to Orochimaru to heal Kimimaro and was later killed by the Edo Tensei of her little brother Nawaki. Shizune was killed by Dan's Edo Tensei at the same time.
Obito's plans would go off without a hitch. One week after the activation of the Infinite Tsukuyomi, everyone died of dehydration