The boss that appears in both Metroid Prime 2 and Metroid Prime 3 is Dark Samus. She is a hostile doppelgänger of Samus and the central antagonist of much of the Metroid Prime storyline.
Dark Samus is created at the end of Metroid Prime when the defeated Metroid Prime takes Samus’s Phazon Suit and reforms into a humanoid body. In Metroid Prime 2: Echoes, she pursues Phazon on the parallel world of Dark Aether and repeatedly confronts Samus, culminating in a final battle as that unstable world collapses.
In Metroid Prime 3: Corruption, Dark Samus becomes the leader of the corrupted Space Pirates and drives the spread of Phazon across the galaxy. She serves as the game’s principal villain and final boss. Players sometimes confuse her with Metroid Prime itself, but Metroid Prime is the original creature; Dark Samus is its later Phazon-created form. Emperor Ing, meanwhile, is the final boss of Prime 2 but does not appear in Prime 3.