outcome
Ezio defeats Rodrigo but chooses not to kill him. The Vault is opened and Minerva speaks to Desmond. Desmond learns that the First Civilization was destroyed by a solar flare, and another is coming.
Assassin's Creed II
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Every route, what unlocks it and what each final choice means.
Assassin's Creed II ends with Ezio sparing Rodrigo Borgia, opening the Vault and meeting Minerva. In the present, Abstergo attacks and Lucy reveals the 2012 solar-flare threat.
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What did you do with Rodrigo Borgia?
What it means
The game's lesson is that revenge is not enough. Ezio's mercy shows that he has become a leader, not just a killer.
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Where this comes from
Every sentence above is built from facts confirmed by at least two independent sources. Sources used: Wikipedia, Assassin's Creed Wiki.