For anyone confused about getting all endings;
Good Ending: Either free Mal0 early and ruin your friendship with Si-Won or release her later and refuse to let her go.
Neutral Ending: Keep Mal0 caged.
True Ending: Release Mal0 later and let her go.
Bad Ending: Don't let Mal0 expand her territory or manipulate real world objects. Free Mal0 later, then refuse to help Zellen in act 3.