In End of Evangelion, Gendo has Adam fused into his hand. However, Rei absorbs Adam into herself (along with part of Gendo's arm) and returns to Lilith.
You have to understand that Rei is made up of cloned material of Yui Ikari and Lilith.
Now... when the two fuse... that's when 3rd Impact begins and everyone is reduced to LCL fluid. HOWEVER due to Shinji's choice, the Lilith entity ends as the big bleeding thing out in the water.
The argument (which I will go along with) is that the Rei-Mind of the Lilith entity is watching over the LCL fluid that is the human race... and that those who have the will for individuality will crawl back out of that muck and mess as Shinji and Asuka have done.