In Metroid Prime, the "Phazon Beam" makes a brief appearance in the second phase of the Metroid Prime battle. When Samus steps into the pools of Phazon that the creature expels, she enters "Hyper-mode" and can damage the creature with the Phazon Beam.
Metroid Prime 2: Echoes
Although Hypermode and the Phazon Beam do not return in Metroid Prime 2: Echoes, a form of Phazon-energized shot is used to defeat Dark Samus in Samus's last fight against her. When Dark Samus releases shots of Phazon energy, Samus is able to draw them in by charging her arm cannon, energizing her next Charge shot with Phazon. This blast is powerful enough to penetrate through Dark Samus's energy shield, which is described as impermeable to any weapon except that of Phazon energy.
Metroid Prime 3: Corruption
The Hyper Beam plays a major role in Metroid Prime 3: Corruption. After Dark Samus corrupts Samus and the other hunters, Samus acquires the PED Suit, allowing her to enter Hypermode and transform her Power Beam into the Hyper Beam at will. She can fire ordinary shots or charge the beam to fire a continuous stream of energy. A fully charged Hyper Beam yields the best damage output in the game, but at the cost of a heavy toll on her Phazon resources, even more than a Hyper Missile.
In Hypermode, a Phazon Meter appears at the top of Samus's HUD and Hypermode will end if Samus empties the bar. Firing the Hyper Beam will empty the bar. Samus consumes about 4 energy for each individual Hyper Beam shot fired.
- "Dark Samus has temporarily become a being of pure yet unstable Phazon energy. She can generate a shield that is invulnerable to all attacks, save one - blasts of Phazon energy itself. Use your Charge Beam to collect Phazon energy that she expels, then fire it back at her. Direct hits will overload and disrupt her essence." —Metroid Prime 2: Echoes Logbook "Dark Samus 4" (Metroid Prime 2: Echoes)