The whole scene is a reference to Adam and Eve, the first male and female. However in a sense this situation is quite the opposite — instead of Heaven, this is Hell, and instead of beginning, this is the end.
Although I didn’t think of it at first, the pieces of wood sticking from the ground at 0:00-0:08 represent graves of all the main characters that died as the result of The Third Impact. We can assume that Shinji built them. Little cross and a can of beer are a reference to Misato, one of the characters of the show who was quite close to Shinji. This represents how much she meant to him and how much he misses her. Also the cross as well as Angels T-posing in the background are a reference to Christianity and Christ being crucified (this show is full of Christianity references, even in the name itself; some fans joke that they had to read the Bible to understand this show’s lore). Also they keep showing the full moon. Why? I think it’s trying to pull our attention to say that the events of this scene take place quite a long time after the events in the scene before, hence in the scene before it was a new moon, but now the moon is full; which is one fact I didn’t notice until doing this log and analysis.