WARNING: This whole thing is a spoiler. Here's my abbreviated best reconstruction of the world of Ergo Proxy. It's the background to the story, and not intended to get into specific mysteries of the series:
Way back when, there was some kind of holocaust (nuclear) the made the planet barren. Some of the humans retreated to a giant spaceship (ark) in orbit. There wasn't room for everybody - it was bad times for the ones that stayed behind.
The retreating humans created 300 Proxies to take care of the place while they were out. The proxies contain an incredible amount of energy, and are capable of impressive feats of strength. They also contain amrita cells, which make them impervious to normal damage. However, very specific, high-energy waves can destroy amrita cells. Proxy's themselves can generate such waves, enabling them to kill each other. Proxies have another weakness - natural sunlight kills them. This is normally not a problem, since the world is shrouded in clouds and all the proxies live in domes anyhow.
Back to the story: After being created, each proxy was programmed to build an artificial womb and create the creatures that lived inside it. The proxies effectively bootstrapped dome creation - the womb made people, people made autoraves, and the combination of the two built the domes and maintained order. However, (this part is conjecture) the humans (psuedohumans?) created by the artificial womb are sterile. They can't reproduce without it. And the artificial womb draws its power from the proxy. So no proxy -> no womb -> no more psuedo-humans.
That last part is important. It means the proxies the lynchpin of the whole system, take them out and it falls apart. Now normally having a single point of failure for a complex system is a bad thing, it makes it very fragile. In this case though, it's a feature. The humans in space want to make sure there's nothing on the ground when they finally come back to rebuild their civilization. To such ends, they built a couple of flaws into the proxies:
1) Proxies have souls/hearts. As a result over a very long time they start to get lonely, since each proxy lives by itself in a dome and has no real peers. This loneliness can cause a couple of different psychological problems:
- Aggressiveness: Proxies become either self-destructive, or homicidal. Either way, the dome that depends on them is in trouble.
- Proxies can become escapist - they flee their domes and try to forget. This will also result in the dome dying.
- Proxies may seek out other proxies to feel less lonely. Which leads to point 2:
2) Proxies are programmed to kill other proxies. In addition to killing off potential resistance for when the space-humans return, this forces proxies to always remain in isolation, adding to the loneliness factor.
3) Proxies die in sunlight. Once the planet recovers, the proxies will no longer be able to live on it.
The story takes place during the last stage of this process - the planet is recovering, and as a result the carefully programmed proxies are beginning to self-destruct. This is referred to as the "heartbeat of awakening;" it's unclear whether the heartbeat is something started in the proxies automatically in response to environmental factors, or if it's being broadcast from the ark in space, though the specific source is not important.
Once the proxies complete their self-destruction, the planet will be clear for the space-humans to return. This is where the series ends, with Vincent outside the remains of the last dome, and the returning human ships descending from the sky.
