Basically I see it being mostly the film slowly developing towards Third Impact (or Fourth perhaps?), but no one actually expects it obviously.
The first part of the film is mainly based around how Asuka is still being contaminated by the Angel - which actually managed to remain hidden and has not been detected in her. Through the first part she seems to get almost increasingly untamed as the Angel consistently contaminates her further and eventually she is finally fully contaminated, and instead of being just mental, it suddenly turns onto her physically - the Angel inside her actually starts to rip her out of her body. She quickly gets the Angel removed form her but she's left lifeless as a result.
For the second part, Kaworu, if he's actually in the film, will start pursuing what he thinks is Adam but is actually Lilith, like in the anime. However, like before he finds out it's not Adam, but instead then remembers all Evas but 01 are actually composed of Adam, so decomposes his Eva Mark 06 to get to the remnants of Adam and start the Third Impact. Once this is realised NERV finds a chance to counter it by using Rei on Lilith, which has a slight chance of forcing out the resulting Impact and reducing the damage. However, unlike what would happen normally in NGE with it somehow working, it actually does go wrong and instead a 'double' Third Impact seems to start. However, when the two explosions seem to come, they suddenly stop and get reabsorbed and stop.
It is revealed that one of the parts of the explosion is, in fact, LCL. However, as it turns out (this is where it gets really suspicious and unknown to everyone but me) that Mari stopped the explosion. It is found out that she is not actually fully human and she has a sort of ability which can take in LCL (which explains why she likes it so much) and therefore remove it. LCL is in fact the main part of the explosion and therefore stopped all of the explosions. This makes them wonder if Mari is actually an Angel, but they cannot find out as she also killed herself along with the explosions. However, they believe she isn't an Angel since there was no such activity in her. Regardless, the question of what Mari really is then remains a mystery...but then, after the credits...
...she appears covered entirely in bandages.
...BTW, has anyone ever thought of saying "Oh my Gendo" instead of "Oh my God"?
