Well, there are three endings. (SPOILERS!!)
The Good ending, which you end up having only if you answer "Infinity" when you're being asked what is death to you, "yes" when you're being asked if Amicus would be a great emperor, and "I think you should talk to him more" (or smth along those lines) when Amicus asks you if he should stick to Neferu. (or at least, score two of these answers.)
The Meera ending, which you end up having only if you answer less than two of the answers above.
The Bad Ending, which you end up having only if you answer "No" when the parents ask you if you'll submit to their benevolent will or something.
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Now, if you have the Good ending, the Parents will show you a vision of you and Amicus, happy, in the future, and you finish the game trusting them (a little). This scene happens, if I recall correctly, on your last day on Adastra (when you visit the archives).
The Meera ending takes place at the same time, same place, but when the Parents are about to show you the vision, Meera, or the Other, we don't know yet, talks to you about how the Parents are evil, and you finish the game not really trusting the Parents.
And finally, the Bad ending, taking place right after Cato slashed your neck. If you answered "Yes" and agreed to work for the Parents, Amicus rushes to save you. And the game continues. If you answered "No", however, the Parents will let you die and the game ends here.