what happened at the ending of the anime Ergo proxy?

i just recently finished watching it.. absolutely loved it but i got lost at times while watching so if anyone could please help me and tell me what exactly happened at the ending of the anime in detail please

Vincent finds himself trapped within Re-l’s consciousness, and observes powerlessly as events unfold. A Cogito outbreak spreads through Romdo and the city falls into chaos. Raul incites the people to revolt, pushing them to hunt down and kill all AutoReivs. As the city continues to crumble, Vincent and Re-l encounter Proxy One. Raul is overcome with regret and despair, and sets out to find Pino. Pieces are played and revelations uncovered as the final fight commences. Monad makes her return and tries to convince Vincent to join her.

Ergo Proxy Anime Music Video