So, to begin...

It's the 44th Millenium. (This lets me give the Space Marines better tech and tactics.) An Inquisition fleet, drawn to NGE Earth by the Second Impact's psychic shockwave, arrives in time to observe daemons appear on NGE Earth through warp portals opened by the Second Impact. The discovery of an exact duplicate of the Solar System shocks the admirals, who recommend an Exterminatus on every planet in the NGE Solar System, but the Inquisitor Lord decides this is the Imperium's chance to undo the damage caused by the Horus Heresy. (The planets in the NGE Solar System are renamed "Shadows of" their WH40K counterparts.) Imperial forces are dispatched to help NGE Earth forces fight off the daemons, as well establishing a unified NGE Earth government under Ikari Gendo. The Adeptus Mechanicus takes away the Evangelions for study.

In 2004, Shinji's foster parents are killed by daemons, and the boy survives only because a Space Wolves claw appeared in time to kill the daemons. (What can I say? I like Space Wolves.) A traumatized Shinji clings to the Space Wolves and begs them to be take him with them. When a rune priest senses that Shinji has psychic potential, he agrees.

Meanwhile, Asuka joins the Adepta Sororitas. When she manifests the ability to project an AT field, she's named a living saint.

In 2015, Sachiel attacks Tokyo-3 and decimates the Imperial Guard forces guarding the city. The Angel is killed by orbital bombardment, which devastates Tokyo-3. Gendo begs the Inquisitor for the Evas' return.

It's now 2027. Shinji, a Blood Claw, is ordered to return to the Shadow of Terra. The Adeptus Mechanicus lets the Space Wolves keep Evangelion Unit 01 as an "Dominator Dreadnought." Shinji arrives in time to fight off Shamshel. The Adepta Sororitas, determined not to let the "abhumans" hog all the glory, gets Evangelion Unit 02 as an "Armor of the Emperor's Wrath." (If you're curious, Rei stays at Gendo's side as a sanctioned psyker.)

Gendo and SEELE continue to plan the Third Impact, thinking the Inquisitor Lord is ignorant of their plans. In fact, the Inquisitor Lord intends to hijack the Third Impact, channel the released souls to the Golden Throne, and resurrect the Emperor.

Comments?

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Please do not make Americans fight giant monsters.

Those gun nuts do not understand the meaning of "overkill," and will simply use weapon after weapon of mass destruction (WMD) until the monster is dead, or until they run out of weapons.

They have more WMD than there are monsters for us to fight. (More insanity here.)

It certainly has an interesting take on things, although I must say that I am fundamentally opposed to combining crossovers with AU (which is to a certain extent what advancing to the 44th millenium so you can change things around means).

Also, your timeline is a bit off, Shinji was born in 2001, and his mother died in the experiment when he was four, so he wouldn't be with his foster parents until at least 2005. I also have to ask how the Evas were made if the Imperium showed up after Second Impact. They would, at best, be considered heretical xenos constructs and at worst dabbling with daemonic forces, both of which end in fire.

That said, STOP STEALING THE THOUGHTS FROM MY MIND! ( )

Shinji + Space Wolves was an idea I was playing around with from before Thousand Shinji. I think it works. Part of the original series was showing how Shinji had hidden monsters within him, as evidenced by Unit 01's proclivity to go berserk. The inner beast of the Space Wolves, and their struggles with it, would definitely mesh well with Shinji's character. Of course, the whole thing was being done rather differently, what with Fuyutsuki actually being the Emperor in disguise and playing Gendo and SEELE for the fools before sealing the Evas and their pilots away for thirty thousand years before digging them out to further his experiments with the Warp after he left the Great Crusade to Horus.

I was planning on having Shinji handed over to Leman Russ for training and Asuka sent to Sanguinius.

Anyway, to sum up, there are elements of your idea I like, and elements I dislike either out of personal preference or because they still seem somewhat disjointed and not quite put together fully. You certainly have the essence of an interesting story going, and with perhaps a little more refinement you could make all the pieces fit together quite nicely.

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I love learning. Teach me. I will listen.
You know, if Christian dogma included a ten-foot tall Jesus walking around in battle armor and smashing retarded cultists with a gaint mace, I might just convert - Noble Ire on Jesus smashing Scientologists

Thanks for the correction. I'll revise the timeline when-- or if-- I begin writing the story.

Simple explanation: the Inquisitor Lord's Sanctioned Psyker interrogated Gendo, found out about the Human Instrumentality Project, erased Gendo's memories of the interrogation, and reported back to her master. The Inquisitor Lord decides to let NERV build the Evas as part of his plan to hijack the Third Impact and use it to resurrect the Emperor.

Yes, Gendo and SEELE are screwed, and thanks to the Inquisitor Lord's Sanctioned Psyker fucking up their minds, they don't realize their scenario has a 13-inch dick up its ass.

Can we say, "Great minds think alike"?

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Please do not make Americans fight giant monsters.

Those gun nuts do not understand the meaning of "overkill," and will simply use weapon after weapon of mass destruction (WMD) until the monster is dead, or until they run out of weapons.

They have more WMD than there are monsters for us to fight. (More insanity here.)