There is one last area in the game to explore; it's small, but it holds the final boss.
Crater Entry Point
This is a small, strange looking cave. Step into the orange circle on the ground to return to the Artifact Temple but there should be no reason to. There is a save station here and it's a good idea to use it since it's the last one available in the game. Even if you don't save it's handy to restore your health after the last battle. There are orange patches behind the save station, not blue like you might expect. Continue to the next room.
Crater Tunnel A
There is radioactive material covering the floor of the this passage. It's similar to Phazon only it's orange and does more damage. (Some call this Orange Phazon but it's not identified in-game.) Lumigeks, Phazon-consuming lizards, swarm into the passage ahead. You'll take damage from the orange material if you try rolling through them, so clear them from a distance. Jump over the radioactive sections of the floor to the exit.
This is a large room with an island surrounded by the orange material. A pillar in the center connects to the ceiling. When you step into the main part of the room you'll encounter Fission Metroids. When attacked they split in two, each having a random beam weakness which you can tell by its color. They take a while to defeat and there's an unending stream of them coming from somewhere, so you're better off just trying to outrun them and only attack if they get too close. As with all Metroids, if they attach to you then drop a bomb to get free. If several swarm you at once then you might want to use a Power Bomb to destroy them, but remember that your supplies are limited.
Immediately get to the tooth-like ledges on the far wall and follow them around to the right. When you reach the end of these there are floating platforms to jump on to reach a ledge in the central pillar. Cross the bridge to a door.
Crater Missile Station
There is a Missile Station here to recover the Missiles used fighting Meta Ridley; you're going to need all the missiles you can get for the upcoming fight. Between the Save Station and the Missile Station you should be at full health and ammo except for whatever you use fighting the Fission Metroids. You might want to backtrack and save again, that way if the worst happens in the upcoming boss battle you won't have to worry about missing scans or refilling Missiles on the retry.
Phazon Core (cont.)
Follow the ledge near the missile station to another platform. Then turn around and follow more platforms to a second ledge in the central pillar. There is a bridge here as well and it leads to the exit.
Crater Tunnel B
This is a tunnel with Spider Ball tracks you can use to avoid the floor. Behind the door lies the fight that will determine the fate of Tallon IV. This is a point of no return so be as prepared as you can be before going through.
Phazon Infusion Chamber
There is a cutscene as you enter. As the door locks behind her, Samus sees what looks like a humongous head hanging from the wall. It soon unfolds into the arachnid-like Metroid Prime, the source of Phazon. After staring down Samus a few seconds, it breaks down the wall and makes off to a more suitable fighting area.
Follow the monster and there is a short cutscene of Samus jumping down to the fight.
Don't forget to get a scan of the monster at some point.
When Metroid Prime is defeated it will fall down a large shaft, but the kill is not yet confirmed. Take a breather then follow it. There is a short cutscene where you look down the hole the monster fell into, then jump down yourself. You see the Phazon melting out of its shell, then what was inside, the core essence, emerges.
Metroid Prime Lair
Don't forget to get a scan of this new version of the monster. This is the last scan in the game so you should get a message saying 100% scans complete.
The core essence is a blue, transparent and octopus-looking entity, but you can still see the triple lobes inside that tell you it's a Metroid.
When Metroid Prime's inner essence is destroyed there is an end of game cutscene. (There are several variations on the ending; we'll cover the 'best' version assuming you've done everything in this guide and have 100%.) First, in a desperate attempt to survive, the monster grabs Samus with one of its tentacles and pulls the Phazon out of Samus' suit, turning it back into the Gravity Suit. What's left of the the monster explodes and causes imminent collapse of the crater.
In some never adequately explained manner, Samus returns to the Artifact Temple and calls her ship to rescue her. As the Temple burns, Samus removes her helmet and looks on with mixed emotions. Mission competed, Samus gets into the ship and rockets to her next destination.
The credits roll, but when they're over the scene returns to Tallon IV where we see a pool of Phazon, and out of it a hand emerges. An eye on the back of the hand opens and we meet an enemy which appears in the sequel.