There are four separate endings based on what you choose at the end;
- "It was something in the water": follow Bill Taggart's ending and cover up the truth, blaming Neuropozyne poisoning as the reason for everything that happened
- "Terrorists did it": follow David Sarif's request and blame Humanity Front
- "I want to believe": follow Hugh Darrrow's request and reveal the truth about what happened to the public
- "The truth is out there": blow it all up by activating the self destruct mechanism aboard Panchaea
Additionally, the narration changes based on how you played the game;
- Evil ending: If you murdered everybody, Jenson will talk about abuse of power
- Neutral ending: If you killed a few people, Jenson will talk about how he tried to do the right thing
- Good ending: If you succeeded at pacifist, Jenson will talk about how the detractors of transhumanisation are wrong in their beliefs
If you're specifically after the neutral endings, don't go crazy with killing people, I'm not sure there are any actual figures available for how many people you have to kill before you're classified as evil, but not purposely going out and murdering everything I saw was how I got the neutral endings.