Can anyone explain the ending?

Ending? I can't even explain the middle!

come to think of it, the beginning is kind of confusing also...

Of course, I live with a Pooka, so my opinion is probably suspect...

“There all in a big computer program” catches the essence of it, I think.

The whole 26 episode series is a sort of “what’s really going on” mystery, done retro/noire detective story style, with giant robots thrown in for no reason I’ve been able to guess other than, well, “who doesn’t like giant robots?”

It throws out various possible answers: that Roger is a schizophrenic houseless man who believes himself a character in a play he’s seen, briefly lapsing into lucidity only to return to his delusion through a triumphal act of will (episode 14); that its all a sociological experiment by Gordon Rosewater conducted in a post-apocalyptic wasteland, with Roger a clone giant robot driver survivor of the apocalypse war (many episodes); that it’s a movie, taking place on a giant set, in which the actors have become too deeply immersed in their roles (last few episodes), and finally that it’s a big computer simulation, possibly with Roger and Angel the only players. At literally the last minute, it throws out a hint that it’s all some sort of black/male/Roger/Big O white/female/Angel/“Big Venus” ying/yang-y thing, with the two essences merging or whatever the **** happens in the end.

It’s pretty clear, I think, that, after the end (Episode 26), everything resets to episode 1, and the whole series plays over, with none of the actors/players/characters the wiser.

Ultimately, I think the writers were going for a “let the viewer chose whatever interpretation they can imagine” ending. Unfortunately for the success of this series, many viewers have, I think, chosen to suspend suspension of disbelief, step back, and chose the interpretation “I’ve just spent 13 hours spread over 2+ years watching something that means nothing at all”.

The best explanation I've come up with after watching this anime many many times is that Roger is actually a homeless bum who's totally out of touch.

However there is a slightly more wild possibility that I thought of that I kind of like.

My second theory is that Roger Smith is an android himself. A pilot left over from a great mecha war. During his last battle he got sunk in the ocean and has shorted. In an effort to find some meaning out of his "life" he creates the fantasy version of Paradigm City. The images of Roger being "assembled" and the fact that he "restarts" the whole thing at the end of the series says to me that it's very possibly all inside his very broken head.

Not as likely as the first theory but for some reason I like it.

I absolutely agree. A computer program with independently contained individually thinking avatars. Something akin to a mash up of "Tron", "Dark City" (although in Dark City it wasn’t virtual, it was staged), "The Matrix" and “The Thirteenth Floor”. The references to “Metropolis” are also very interesting, given the android characters, particularly Dorothy, but I think that’s more an influence from the creator’s/programmer’s mind.

To expound upon this, it’s a computer program that Angel (or the virtual entity known as Angel, which may be modeled after a real person) herself may be the creator of (or at least a participating programmer of), who then attempted to test it by plugging herself into it, only to suffer some form of catastrophic accident. If this is true and Angel began as an external user of the programmed world that at some point (represented by the 40 year time span since the memory loss) was catastrophically "disconnected", then at that time either her mind became lost in the virtual world, or a representation of the user/creator's mind manifested itself as Angel (I think it would be the latter).

Regardless of anything else presented in the entire series, of any of the mythology established within the framework of the universe we’re shown, there is one key moment in Episode 26 that reveals the true nature of the reality presented: Angel as big Venus, after learning the true nature of herself and the reality around her, begins to “erase” or “derez” that very reality as she lumbers along, not destroying but more “unmaking” everything that she may very well have had a hand in creating herself. This ability puts her at the center of everything, and although there are hints throughout the series that everything is virtual or at least staged, this one event irrefutably reveals that it’s either all virtual or all in someone’s head (i.e. a dream, a delusion ala “Identity”, etc.) I think this was definitely a simulation and not a dream, however, evidenced by what was happening as Big Venus “derezzed” reality, leaving behind what looked very much like the holodeck from “Start Trek: The Next Generation” or even the lightcycle arenas from “Tron”. This one Big Venus scene ultimately clenches the nature of what’s actually going on. It’s a computer simulation, possibly a game or just an experimental attempt to simulate individually thinking, self-aware entities within a virtual world, and possibly a combination of those two, that’s somehow run away with itself and gone awry.

Until the end, that is, when a virtually simulated Roger Smith convinces the real-world-modeled avatar Angel that living, yes “living”, on as they had been is preferable to ceasing to exist since what they’ve become are in effect their own form of life, life that is precious and worth preserving. This hints that Roger is either himself based on a real-world person, or is a simulation that transcends his original creation into a self-aware state of mind powerful enough that he begins to understand that he is himself in fact just a simulation, but that regardless of that fact has become a lifeform in his own right, along with the rest of Paradigm City. How else could he make the choice to continue on with the lives they had without also knowing in that moment that they were only virtual? It’s his resolve, and the choice that he makes, that calms the collective chaos of the virtual world so that it can then “normalize”, suggesting that everyone in this world is interconnected, which solidifies it as a single computer program, even if it is populated with individually thinking virtual entities. It could be speculated that Roger is the simulation of a real-world user as well, or that every entity in the virtual worlds is. There's not enough information to conclusively determine this one way or the other, although ultimately it doesn't really matter if only Angel, and possibly Roger, were avatars for real-world people, or if everyone was.

It could also be speculated that the real-world counterpart of Angel is still in fact plugged into the simulation (like “The Cell” or “The Matrix”) in a comatose state. However, I think the “clipped wings” depiction (shown by the scars on her back, enhanced by several things the old man says, and what we’re shown when she enters the virtual space in the room at the bottom where the elevator lets them off at), strongly suggests that a real-world connection no longer exists, and that the virtual reality we see has become completely autonomous and self-sustaining in some fashion.

To conclude this theory, I surmise that the events shown throughout the season are the results of actions taken by the collective virtual consciousness of all the entities in this virtual world as a whole, with the individually thinking constituent components unaware that they are really all part of the same single meta-entity. It's as if the program itself is attempting to self-actuate, e.g. to figure itself out, to come to terms with itself, to make sense of the nature of its existence, and to then determine how it wants to proceed in the future (i.e. if it values itself enough to continue existing or to shut itself down). The individual constituent entities of Roger and Dorothy are pivotal to the success of the collective whole by themselves transcending their own natures and finding the strength to continue on despite logic dictating they shouldn’t be able to. It’s their strength, their established emotionally-based bond with each other, and then in turn Roger’s bond with Angel (who lies at the core of, and may ultimately actually be, the meta-entity), that starts the process resulting in the entire virtual reality finding peace with itself and stabilizing or even maturing, becoming a self-contained living, breathing universe, like a child Artificial Intelligence struggling through adolescence and then finally becoming an adult.
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"I'm something new entirely. With my own set of rules. I'm Dexter."

Actually, the show does not reset itself in the end. If you notice when Roger drives off and they show the aftermath of the battle between Big Fau and Big O. Roger was able to reach negotiations with angel or save her humanity and instead of resetting everything, she gave the people of paradigm another chance and she wrote herself into Roger's life.

I always thought 2 things about.

One that it was program and roger was self aware, and towards the end the program was either resetting itself or cleaning the area for a new program to run. I can see how some say that roger basically saved his virtual world, maybe even made it larger.

That or it was a tv show, and that by resetting it they can have a new series that plays out differently. That is until roger got wise that something wasn't quite right.