I haven't watched the end of Gantz, but I have watched enough anime series to know that the exact same thing happens in the end. So for the benefit of yourself I'll condense it down and hopefully it'll correlate with your desire for an explanation.

A is the protagonist, comprised of different characters or factions. B is the first antagonist, comprised of different characters, factions and usually an unknown element. C is the true antagonist, which turns out to be a derivative of the unknown element of B. A and B fight for a bit, then A realises B isn't really the enemy, so starts fighting C. A and C duke it out. Now one of four possible scenarios occurs;

1. Everyone dies due to a large explosion/bullets/lasers/etc
2. Everyone evolves into a higher state of being
3. One of the people within A dies due to a large explosion/bullets/lasers/etc
4. One of the people within A evolves into a higher state of being

Obviously if 1 occurs, simultaneously 3 occurs, as is the same for 2 and 4. On occasion 1 and 4 may occur in that the person described in 4 is exempt from the fate described in 1. The death thing is obvious enough. The evolution thing can take on many forms but often involves the person either turning into pure energy, some new biological entity through the melding of another species, or a new technological entity through the melding of a piece of technology of some description. It is common for this fate to be shown through obscure images and vague narrative descriptions. Hence the confusion that tends to occur.

Hope that helps.