DISCLAIMER: I'd don't own any of the characters of Lord of the Rings, Naruto, Marvel, DC or Star Wars or Star Trek
Simplified the Plot: Middle-earth becomes Ninja World. The Ninja World becomes the Marvel World. The Marvel world becomes the DC World. Naruto will have visions of Star Trek and Star Wars
1. Smaug was actually a female dragon but got raped by other monster. Smaug she lay a egg. Arwen and Aragorn's kid married Galadriel's and Main Dwarf's child. Decades and Centuries go by. One of there descendents becomes know as the Sage of the Sixth Paths.
2. The Sage of the Sixth Path was near to the volcano when Smaug had lay the egg. The power of all of the rings running through the Jubi.
Naruto's world goes mostly close to the cannon until the end of the Fourth Ninja war. Konoha gave all the eyes that Kabuto, Sasuke, Orochimaru, Madara, Obito stolen and all of the different Bloodlines from other Villages. Naruto can use all of the bloodlines. After the mixture of bloodline and the sealed the tailed beasts and skeleton of the Jubi into his own body like Mito Uzumaki did. Naruto married Sakura Haruno, Yamanaka Ino, Hyuga Hinata, Inuzuka Hana, Uzuki Yugao, Isarabi, Kurama Yakumo, Kazahana Koyuki, Toki, Shion, Hokuto, Temari, Kurotsuhi, Karui, Terumi Mei and Mitarashi Anko due to C.R.A. was place onto him by the Elemental Council and the Shinobi Alliance.
Unbeknownst to the females and Naruto. Naruto and them are the Father and Mothers of the X-Genres that'll show up in Marvel Universe.
3. After Naruto dies in his time. Mr. Sinister finds out about his heritage and the Father of the X-Genre. He goes to the forbidden part of the Currently the Japan. Durning the fight of Logan and Silver Samurai. Those enter the forbidden place of Japan to see Mr. Sinister taking Naruto's coffin away. The Samurai told Logan about the body in the coffin is what's the left of Japan's Ninja way. He was the Hero of Heroes in his time. So Logan and Silver Samurai tries to stop Mr. Sinister.
4. Sinister injected Naruto's body with Gambit's power, Pyslocke's power, Nightcrawler's power, and Magneto's power. Sinister will do what the X-Program did to Wolverine but more dangerously. Sinister injected the metal alloy adamntium with golden, silver, Bronze, Cooper, led, iron, platinum, zinc, Led ,Diamond, Ruby, nickel and tin.
5. Brotherhood, Hellclub, X-Men, Warlocks and every mutant on the planet could felt the power of Naruto's Mutant power activated. They all came to recuse the Father of X-Genres.
6. Lilandra, Phoenix, Mystique, Rogue, Scarlet Witch and Storm married Naruto.
7. Apocalypse refused to believe that Naruto is the Father of X-Genre cause he'd think he is the Father of the Mutants.
8. Naruto sealed the Apocalypse up into himself. That cost nasty side effect. That led is part of Naruto's skin now. Naruto's hair color becomes like Ino's Platinum blonde color and Temari's hair color mixed. Naruto has Nightcrawler's ear shape but his skin color becomes bronze. Naruto's eyes become blue diamond color.
9. Apocalypse frozen Naruto in that state.
10. Few more Centuries and few more decades later. After Alien Invasion and Thanagarians Invasion. Martian Manhunter hears the Mental cries of Naruto.