There should be this stupid convoluted series of actions you have to do throughout the entire game, starting as soon as you get off the train. Like talk the potion guy, grab the phoenix down and eat the babies, play Inna Gadda Da Vida on the piano, and so on until you get back to the Ancient Capital in Disk 3 and click on the pool seven times and Aeris' corpse will rise out and then when it looks like everyone is finally reunited the Cheese Weapon pops out of her Xenomorph style.