The Fusion Core (as named in the Metroid Prime Nintendo Power comics) was the main reactor of the Frigate Orpheon. Located at the center of the Reactor Core, it powered the ship and its systems. A spinning energy shield protected the Fusion Core from interference.
At some point prior to Samus Aran's arrival on the Orpheon at the beginning of Metroid Prime, the third and only surviving Parasite Queen took up residence in the Core. Samus encountered the Queen and battled it above the Core, with the beast utilizing the reactor shields to defend itself from Samus's attacks. Samus used gaps in the shielding against the Queen and weakened it. It fell into the Fusion Core, which ruptured and went critical moments later. Samus escaped the ship before the reactor meltdown, but not without cost. A power surge from the Queen's descent into the Core downgraded Samus's Varia Suit to her basic Power Suit and caused her to lose several of her abilities.
Closer analysis of the Fusion Core shows it to emanate purplish electricity. Its rim is surrounded by mysterious jagged, orange-colored crystals.