The Space Pirate Experiment
The Space Pirates actually creating several Parasite Queens by enhancing their bodies with Phazon. This was one of their first experiments involving Phazon.
One Parasite Queen went rogue and wrecked the ship to a point of no repair, and the Space Pirates sent out a distress call to more Pirates to come and help them contain the Queens and clean up the mess. Unfortunately for them, the distress call was picked up by Samus Aran, their worst enemy. She scoured the ship, killed some weak Pirates, and then was confronted by two Parasite Queens - one dead at the entrance, and one whose lifesigns were flatline, in a stasis tank. She also picked up some Lore concerning what had happened with the Pirates following the destruction of planet Zebes.
When Samus reached the core of the frigate, she found four Space Pirates dead as if they had been in a scramble to escape from something. She entered the Main Reactor, and their killer was revealed.
The Parasite Queen attacks by firing blasts of plasma from her mouth. Samus must shoot the mouth to kill her. After a bit, the Queen will make the radiation shields spin round her, blocking her weakness, but Samus can exploit this by dodging rapidly. Samus can use any weapon to injure the Queen and after awhile, the Queen will overload and crash into the Reactor Core below her and cause a malfunction in the ship's computers, setting off a detonation sequence.
Metroid Prime 3: Corruption