When Samus Aran enters the table, the Force Ball upgrade will be waiting for her. To collect it, the ball must be launched at the glass encasing the upgrade. Once collected, the Metroid Prime will suddenly drop from the ceiling, commencing the final boss battle.
To defeat the Metroid Prime, Samus must launch herself around it, lighting up all the blue lights, filling in the S-A-M-U-S Lights and allowing Samus to enter Combat Mode. (Samus can also use one of two Award Scanners on the table to enable Combat Mode) Missile shots must be fired at Prime to move one of its legs, allowing Samus to enter a Force Ball charger, charging her Force Ball and activating it for use on Prime. Eventually, the exoskeleton of Metroid Prime will explode, revealing the core essence. The battle will remain the same (though Metroid Prime will have new attacks). Once the second form is defeated, Metroid Prime will be defeated, ending the game. During and before the battle, Metroids may randomly appear on the stage.
- Despite being based on the Impact Crater, the Phazon Mines theme is heard on the table instead. The Impact Crater theme is instead heard in the Metroid Mania minigame.
- Jennifer Hale voiced Samus' grunts of pain in the Prime series games. The only time these are heard in Pinball is on this table.
|Elements of Metroid Prime Pinball|
|Tables|| Pirate Frigate • Tallon Overworld • Phendrana Drifts • Phazon Mines • Artifact Temple • Impact Crater |
|Board Features||Clone Machine • Flashing Lights • Hurry Up • Progress Bar • Drop Target • Cow|
|Mini-Games|| Beetle Blast • Burrower Bash • Clone Multiball • Gunship Multiball • Metroid Mania • Parasite Purge |
Phazon Frenzy • Phazon Multiball • Shriekbat Shootout • Space Pirate Panic • Triclops Terror • Wall Jump
|Other||Jackpot • Bounty Multiplier|