When Samus first enters the Core room, Mogenar is being fed energy by the Leviathan Core. When Samus approaches it, it grabs four red orbs from around the room and generates four Phazon cores, three on its front around its head, and one on its back, directly behind its head. These red orbs are its weak points. It hides the orbs behind shields periodically, preventing Samus from damaging it. It also frequently switches the placement of its orbs in order to prevent Samus from damaging the same orb for too long.
When an orb is destroyed, then Samus must enter Hypermode and blast away at the shining light. When Mogenar loses an orb, it sometimes releases ghostly green hands to retrieve more orbs from the edge of the arena.
Mogenar attacks by jumping up and down with both its feet, creating a shockwave that travels in a circular pattern away from the impact. It also stomps the ground with one foot sometimes, creating a shockwave that travels in a straight line towards Samus. It also attacks by charging towards Samus, ramming her into the wall. After one of its orbs is destroyed, it generates Phazon plating around its feet and begins charging more frequently. Samus must destroy the Phazon plating with Morph Ball Bombs.
After destroying all four Phazon cores completely, Mogenar is defeated, revealing the Hyper Ball.
- The unlockable Diorama depicting the Mogenar battle shows a Reptilicus watching from a distance, suggesting that Samus was monitored through her battle.
- There are several other Mogenar-Class War Golems found throughout Bryyo, but these are always inactive or docile.
- "Ancient Reptilicus War Golem appears to be receiving energy from the core of the Seed. Corrupted War Golem reanimated and energized with Phazon. Relies on socketed energy orbs as a source of power. The orbs themselves have a fragile exterior but contain pure Phazon energy within. This energy must be completely overloaded before it will be destroyed. Eliminating all power sources is the only way to bring Mogenar offline." —Logbook (Metroid Prime 3: Corruption)