In Metroid Prime, the Frigate Orpheon is the first stage that Samus Aran will explore after receiving a distress signal. She'll soon come to find that the entire crew, or most of it, has been killed, with the source being the mutated Queen Parasite, which is not only represented in this game but also in the Brawl stage as well. At the end she'll battle the beast who'll then crash through the ship, thus destroying it.
Super Smash Bros. Brawl
It takes place in the beginning area of Metroid Prime, and in the background you'll see the Parasite Queen, who will not attack. After fighting for a bit, the lights will go off, making the battle more intense than ever. Eventually, the whole stage will flip 180 degrees and you'll have to fight on the opposite side. You will not get hurt when you flip, but you may get K.O.ed.