The Far Cry series does not provide you with a lot of choices. However, the games tend to allow you to dictate what ending you get. In the case of Far Cry 3, you have two distinct options as there's no secret conclusion in this one unlike some of the others.
Yet, the choice doesn't come when you may expect it. You have to defeat both Vaas and Hoyt before any decision is made. This endgame begins with the Rakyat kidnapping your friends and you going to Citra's Temple to confront them. Here are the two ways things can play out.
Stay On The Island With Citra (Bad Ending)
When you reach the Temple, Citra attempts to be-witch you. She professes her love to you and asks you to stay with her on the dangerous island. The woman then blows some magical dust in your face, which takes you to a strange place where you're handed a fancy knife. The next thing you know, that same knife is pressed against Liza's neck. If you want to stay with Citra, you simply pick to join her.
Spoilers FollowThis decision prompts you to slit poor Liza's throat, killing her instantly. Then you and Citra have a romantic encounter as she intends to have your child. She clearly doesn't see a future with you, though, as she kills you after the deed is done. Your death serves as the last moment of the game.
Set Your Friends Free (Good Ending)
The setup to this ending is exactly the same as the other as Citra confesses her feelings towards you before blowing magic dust in your face. She then encourages you to kill your girlfriend. But you have the option to save your friends instead.
Spoilers FollowIf you choose to rescue your allies, Citra will naturally be upset and beg you to stay. Dennis, on the other hand, will be filled with rage because you rejected Citra. So, he charges at you with a knife, but Citra jumps in front of the blade, taking the stabbing in your stead. While dying, she still professes her love and asks you not to leave. Both you and Dennis apologize to her as she passes away. Then you and your friends leave the island as your character, Jason, gives one final monologue lamenting all the killing he's done.