'The Creator' says that he died, but something pulled him back and gave him his powers.
In the intro we see how his home is struck by a meteor shower, with each meteor having these red crystals stuck to them.
The save crystals are also red.
Now, saying that they gave Naija powers is a bit of a stretch at best, but they sure are good for coming back from the dead.
Could this perhaps be a future plot element? Wherever they came from might be our ultimate destination. And dead things being brought alive is always useful for creating enemies and bosses.
Maybe I'm just influenced by my initial expectation of the ending... I thought Naija ended up stuck in the crystal seen in the title screen, and the boy touches it as he falls into the water, thus all her memories (our adventures) flashing into his mind, moments before he drowns..