Probably the most cinematic and story-altering parts of the game change the outcome of the game's ending. In Parasite Eve 2, certain actions determine Aya's result at the end of the game.

Good Ending - Pierce
1. Flint Must Be Alive After the battle with Cannon-Mouth.
2. Return To Dryfield Upon Defeating the Trash-Monster, Meet Pierce Tower - Don't Go To Elevator.
3. With The Conversation With Pierce, Go To the Pod Servivce Gantry. Read Message an Call Right Away.
4. At Tent, Use the Teddy Bar On Flint.
5. Upon rentry, save Pierce.

Normal Ending - Kyle
1. Don't Return To Dryfield.