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In Metroid Prime

The Frigate Orpheon was a transport and research frigate which was used by the Space Pirate Science Team to to house and perform tests on a number of unusual alien species, including Meta-Ridley and the Parasite Queen. It is also notable that the ship contained a noticeable amount of Phazon. The vessel was key in the transportation of the Metroid samples from the destroyed Space Pirate base on Zebes to Tallon IV. The ship was rendered immobile while in orbit over Tallon IV, due to the fusion core failing when a dying Parasite Queen fell into it. 
At the beginning of Metroid Prime, Samus receives a distress signal from the Frigate Orpheon and boards the ship in response. Samus fights her way through the ship, defeating the remaining the Space Pirates, until she finds the Parasite Queen in the reactor core and kills it. Samus then escapes the ship, catching a brief glimpse of a fleeing Meta-Ridley, before the ship crashes onto the surface of Tallon IV. Samus returns to the wreckage of the ship later in the game to make her way through it to reach the Phazon Mines of Tallon IV.

In Other Games

Frigate Orpheon is a stage in Super Smash Bros. Brawl which is set in the reactor core of the Frigate Orpheon. The Parasite Queen from Metroid Prime can be seen in the background, overseeing the stage. Periodically, alarms will also go off on the stage and it will be flipped 180 degrees. 

The stage Pirate Frigate in Metroid Prime Pinball was also based off of the Frigate Orpheon.

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