Everything in the show is a dream of Pen-Pen the penguin, who is God.
He's so conspicuous and out of place in the storyline that there must be some greater reason for his existence. In addition, the whole world seems to be designed for his comfort, and he's the only member of the cast who is not screwed up.- ...So Pen-Pen is Mokona?
Pen Pen was trying to prevent third impact
Cute animal mascot in what ended up bieng a very dark and mindscrewing series? Pen Pen was actually trying to lighten things up and help everyone keep things together so that they would be in better shape mentally and stop Seele's plans (Penguins don't like for the oceans to be full of tang). Sadly Misato sent him away at a critical juncture, and screwed it up.Pen-Pen is actually a fusion of the soul of Misato's father with a random penguin, caused by the energies of Second Impact.
What? It makes just about as much sense as half the Canon stuff.- FINALLY! Someone appreciates how important Pen-Pen really was.
Pen-Pen was found at Adam's dig site.
Misato took him in after NERV got bored of keeping him under surveillance in case he did something interesting. Rei/Mari/Kaworu will have a Pen Pen encounter
Thus far in the Rebuild movies both Shinji and Asuka have had comical encounters with Pen-Pen in the bathroon. At some point in the remaining two movies, the joke will be continued in some way with the at least one of the remaining children.- Kaworu will be able to speak Penguin.
- There will be a scene where the two discuss what would be needed to make Shinji happy, and whether he should end up with Rei or Asuka.
- There is already fanart about Mari falling victim to this... Rei won't as she has no sense of modesty.
Pen-Pen is actually Cthulhu
Think about it. It makes sense. Antarctica was utterly destroyed, and Tierra del Fuego and other non-antarctic locations are probably destroyed too. In the aftermath of the Second Impact, it's almost certain that noone was maintaining zoos, thus, penguins are also dead. Thus, Pen-Pen is a Great Old One, and also, the Zeroth Angel. All of the other angels are simply lesser entities Pen-Pen calls up. Why is Pen-Pen seen as a penguin? Because his true form would drive men insane, so the cast's minds instinctively change it to something else. Finally, it handily explains all of the Nightmare Fuel if a Great Old One is behind the scenes. The Episode 26: Pen-Pen is a celebrity with a massive merchandising empire.
Hence why Shinji has a Pen-Pen bobblehead. Also because Pen-Pen is awesome, and the idea of TV-star Pen-Pen is too epic to ignore. Pen-Pen is Jesus.
Hence why everything fell apart when he left. Pen-Pen is the only being to not initially fall into Instrumentality, and is there before Asuka and Shinji.
Pen-Pen is a gigachad who has managed to already work out his emotional issues and remanifest his individual will before the series began. Instrumentality will not remotely work on him.