Samus quickly escapes via the ventilation network, but not before an explosion damages her suit, causing the Varia Suit, Charge Beam, Missiles, Morph Ball, and Grapple Beam to malfunction, leaving only the Power Suit and the Power Beam. She witnesses Ridley, genetically rebuilt after Samus' fight with him on Zebes, fly off towards Tallon IV. Once she gets to her ship, Samus follows, eager to destroy the Space Pirates once and for all.
After landing in the Tallon Overworld, Samus explores nearby areas of Tallon IV, such as the Chozo Ruins.
In the Chozo Ruins, Samus finds that the local water supply has become extremely toxic, harming her even through her Power Suit. As she explores the ruins, she regains many of her lost abilities and learns that the Chozo on the planet had been killed or corrupted by a great poison brought to Tallon IV on a meteor many years ago. Eventually, Samus discovers the source of the toxic waters, which is located in the ruins. She destroys Flaahgra, a heavily mutated plant, and purifies the spring.
Samus next visits Magmoor Caverns and discovers that the Space Pirates are drawing large amounts of geothermal energy from the region. Samus leaves the caverns and arrives in the Phendrana Drifts, an icy area once home to another Chozo enclave. Samus acquires more abilities there, and soon infiltrates the main Space Pirate laboratories. Her arrival catches the Pirates off guard; they were unaware of her presence on Tallon IV, and the laboratories had relatively few guards. After fighting her way through the labs, Samus discovers that the Pirates have been conducting experiments with Phazon, the great poison the Chozo spoke of. She also finds out that the Space Pirates had brought some Metroids that had survived the destruction of Tourian to the planet. She then confronts Thardus, a Phazon entity brought to life by Space Pirate experiments. She defeats Thardus and continues on.
With her new abilities, Samus re-explores the places on Tallon IV where she has already been, like the Chozo Ruins. She soon begins to encounter the spirits of Chozo corrupted by Phazon. As she continues, Samus finds the wreckage of the Space Pirate Frigate Orpheon, which had crashed into Tallon after its destruction. A massive operation is underway by the Pirates to try and salvage what they can from it, including some Phazon. Samus once again travels through the Orpheon. Upon emerging on the other side, she discovers the entrance to the Space Pirate Phazon Mines.
Samus enters the Phazon Mines, encountering massive amounts of Phazon and heavy Pirate defenses. She also discovers the outcome of the Phazon experimentation project: Elite Pirates, Pirates mutated to huge and dangerous forms with Phazon infusions. Later, she also learns of two other Phazon-based creatures: the Omega Pirate, an Elite Pirate that had grown to enormous size and power through its near-limitless capacity to absorb Phazon, and the Metroid Prime, a creature that had come to Tallon IV with the original meteor. The Metroid Prime was genetically similar to Metroids, though much more developed. Like the Omega Pirate, there was no limit to its ability to absorb Phazon, but in this case, the massive doses of Phazon had absolutely no side effects. The Pirates had discovered the creature in their mining projects, and captured and studied it. They infused it with much Phazon in the hopes of creating an ultimate weapon, but the creature escaped back to its den. The Metroid Prime was the guardian of the Phazon core on the planet; while the creature survived, the Phazon could never be purged from the planet.
Samus soon reaches the lowest level of the mines. On this level, the Pirates had been conducting many experiments with their remaining Metroids. These Metroids had been so heavily mutated by Phazon that they no longer followed the natural life cycle of their species, instead forgoing all metamorphoses in favor of remaining in their larval stages. Samus fights her way through the Metroids and reaches the Omega Pirate. She defeats it, but as it dies, it collapses on her and dissolves into Phazon, which is absorbed into her Power Suit, creating the Phazon Suit. It provides Samus with immunity to Phazon, and is even capable of harnessing pure Phazon as a weapon.
With the Pirate operations in shambles, Samus sets out to find a way to rid the planet of Phazon. She discovers the ancient Chozo Temple, which contains a lock that prevents access to the meteor's Impact Crater. The deceased Chozo had built this Cipher to contain most of the Phazon within the crater, but some was still able to seep out and begin to corrupt the environment. Samus learns that in order to break the shield and access the crater, she must collect and unite twelve artifacts known as the Cipher. After much journeying and trouble, Samus unites the Cipher and prepares to fight the Metroid Prime. The central totem begins to lower the shield...
...but Meta Ridley flies in and destroys the totems and the Cipher. All hope of entering the crater appears lost, and Samus is forced to fight her nemesis once again. When Samus is about to strike the final blow, however, the Chozo statues on the temple come to life and blast Ridley with lasers and cause him to fall off the temple, leaving him for dead. The Chozo Ghosts inside the original twelve totems (who were uncorrupted by Phazon) then use their collective energy to lower the shield and create a pathway to the Impact Crater, recognizing that Samus is their only hope.
In the Impact Crater, Samus encounters many heavily mutated creatures, including many Metroids. Samus soon finds Metroid Prime, a hideously mutated Metroid, and the which realizes that Samus is a major threat. Samus engages in a tough battle, but she eventually comes out on top. The Metroid Prime falls off a cliff, but Samus follows, not taking any chances. Indeed, when she discovers its apparently dead body, the core essence of the creature flies out, abandoning its shell and engaging Samus in its true form. Samus uses the abilities of her Phazon Suit to overload the creature with pure Phazon. In a last, desperate move, the dying Metroid Prime changes form again and absorbs Samus's Phazon Suit. It then explodes, releasing all of the Phazon in its body into the Phazon Core, sending it into a critical overload. Samus barely escapes and calls in her Gunship. She then removes her helmet to watch as the crater collapses in on itself, purging all of the Phazon from Tallon IV. She then flies off to search for a new bounty to claim.
Some time after Samus leaves, a small puddle of Phazon is all that is left in the remains of the crater. Out of the puddle rises a hand wearing something that looks similar to Samus's Phazon Suit. On the back of the hand is an eye which looks around warily...
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