Depending on what you do during the game you'll see one of four main endings, here's how to get them:

ApostleCorp Great Advance
Upload Aquinas Spec to JC Denton, use the machine at the base of the statue and keep JC Denton alive.

Illuminati Age of Light
Upload the Aquinas Spec to Illuminati, destroy the machine at base of statue, kill JC and Paul Denton and keep either or both Chad and Nicolette alive.

Omar Invasion
Don't upload the Aquinas Spec to anyone, destroy the machine at the base of the statue and kill the leaders of all factions.

The Templar Flood
Upload Aquinas Spec to the Templars, use the machine at the base of the statue, kill both JC and Paul Denton and keep Saman alive.