Found this one courtesy of the TV Tropes fic recommendation page for Evangelion:
Deus Ex Evangelion. After Shinji Ikari dies fighting the third Angel, Asuka is brought from Germany and made the pilot of Unit 1... only to discover a presence within the great war machine. A well-done elseworld with a very cool premise. Incomplete, but the most recent chapter was added just a month or so ago.
-- Bob
---------
Then the horns kicked in...
...and my shoes began to squeak.
Deus Ex Evangelion. After Shinji Ikari dies fighting the third Angel, Asuka is brought from Germany and made the pilot of Unit 1... only to discover a presence within the great war machine. A well-done elseworld with a very cool premise. Incomplete, but the most recent chapter was added just a month or so ago.
-- Bob
---------
Then the horns kicked in...
...and my shoes began to squeak.