Dark Samus

Metroid Prime is the title character and the main antagonist of the Metroid Prime trilogy. The first two installments of the Metroid Prime story revealed little information pertaining to Metroid Prime’s past. According to in-game evidence, Metroid Prime is a native of Phaaze, not SR388. Additional logs from the game reveal that the Chozo race encountered the creature long before the events of the game. The game strongly implies that Metroid Prime was the leading cause of the Chozo's decline on Tallon IV.

Prime arrives on Tallon IV long before the initial events of Metroid Prime. Samus Aran, the protagonist of the Metroid series, encounters the creature while investigating Space Pirates operations on the planet. Amidst the struggle, Samus discovers the ruins of Chozo civilization, and learns about an astronomical object that brought the once glorious and peaceful society to near extinction.

Depending on the regional version of the game, there are two scenarios pertaining to Prime’s involvement with the Space Pirates. According to the North American version, the pirates capture Prime for an unspecified amount of time, but in the European and Japanese versions they are only able to detect its bio-signs. Furthermore, the North American release goes on to state Metroid Prime's name is eponymous to the Metroid species, due to unmistakable genetic similarities. Because the Space Pirates fail to capture Metroid Prime in the European and Japanese versions of the game, the whereabouts of Metroid Prime's name and how it came about its weapons are more inconsistent compared to its North American counterpart. However, the North American version features a plothole in that Metroid Prime was captured yet the Space Pirates in game are trying to find a way to get into the impact Crater, regardless of the fact that they would have done that to capture Prime.

In Metroid Prime 3: Corruption Samus encounters the same exoskeletal shells that were present on Metroid Prime's first form, confirming Prime's origin's from Phaaze. However, this is only half the story, Log information on the infant Leviathan creature encountered on Phaaze reveals that, once a Leviathan reaches adulthood, it is sent into space instinctively within it's womb to spread Phazon across a far away planet. Once there, the core will start to corrupt the planet but die in the process. It then goes on to say that, before death, it "convinces" any large creatures to protect the seed while the process of corruption takes place by exposing it to large amounts of phazon, thus being able to control it. One can safely assume that a Metroid was this creature, it's core essence highly resembles a mutated Metroid, probably due to the said Phazon exposure. The log also addresses that the exoskeletal shell is a sort of armor for the chosen creature. Ultimately resulting in Metroid Prime.

Physiology
Metroid Prime will duel Samus using two forms, the first being a heavily armored insectoid form, vaguely reminiscent of an Alpha or Gamma Metroid, and the second a phantasmal form reminiscent of a regular Metroid. Despite the two physically diverse variations, Metroid Prime statically retains its signature characteristic to stare through Samus with a piercing neon gaze.

Exoskeletal form
Samus first encounters Metroid Prime deep within Tallon IV's “impact crater” in its exoskeletal form. While this form is already lethal in terms of size and relatively explicit strength and dexterity, it has undergone much transformation to develop special energy attacks that mimic Samus’ elemental power beam variations.

Furthermore, due to an advantageous genetic flaw, Metroid Prime has developed the ability to screen various weapon attacks by altering its chemical build. In other words, Metroid Prime is able to become temporarily invulnerable to all but one of Samus’ beam weapons at a time, denoted by the color of its exoskeleton. However, despite possessing such a powerful characteristic, the genetic flaw acts as an Achilles heel, limiting the utilization of only one elemental weapon per phase. While in this form Metroid Prime attacks by shooting powerful beams from a mouthlike hinge on the bottom of its shell. It also shoots energy orbs that can be destroyed by the corresponding beam (or one missile) to what attack form Metroid Prime is in at the time, usually leaving behind missiles and energy pick ups.

An interesting note about this form is that unlike all other substances and enemies that deflect a beam or missile they are not vulnerable to, shots that are deflected from Metroid Prime's shell (or miss its weak spot) can damage Samus. However, this was changed in the European and Japanese versions, and no longer has this unique feature.

Samus was able to damage this exoskeleton by shooting the appropriate beam for the current screen into what appears to be the eyes of the beast. After chasing Exoskeletal Metroid Prime through multiple identical chambers under the Impact Crater, the exoskeleton fell into Metroid Prime's lair where it revealed the Core Essence of Metroid Prime by abandoning the exoskeleton on the floor of the lair.

According to Metroid Prime’s log entry, it has mysteriously assimilated various mechanical devices into its body. While the North American version of the game suggests Metroid Prime acquired this technology from the Space Pirates after being captured by them and subsequently escaping, the European version differs slightly, making no mention of this, along with having never been captured by the Space Pirates. Due to Samus’ intervention with the Space Pirates on Tallon IV, all research regarding Metroid Prime has presumably been destroyed.

Core form
After Samus is able to beat Metroid Prime’s exoskeleton form, it will reveal its “core essence”. This form of Metroid Prime resembles a Metroid, although it possesses a somewhat humanoid face and does not possess the pincers that regular Metroids have.

Unlike its preceding form, Metroid Prime is permanently impervious to all of Samus’ weapons. Furthermore, the entity can bend light, leaving it invisible to the naked eye without the aid from an x-ray or infrared device. Also, Metroid Prime is capable of secreting puddles of Phazon, as well as producing Hunter and Fission Metroids.

By using these puddles as a source of corrupt energy, Samus can momentarily utilize her Phazon Beam, and deal large amounts of damage to Metroid Prime. After delivering a catastrophic blast of Phazon energy, Samus is able to send Metroid Prime into a state of extreme molecular instability, leading it to revert to a mere pulp of Phazon. As Samus attempts to leave the doomed battle site, a tentacle snakes out from the remains of Metroid Prime, absorbs Samus' Phazon Suit, and explodes.

Dark Samus
In its death throes following its defeat on Tallon IV, Metroid Prime sucks off the outer layer of Phazon which composed Samus's Phazon Suit, absorbing it and using it as a shell to form Dark Samus. Prime gained new abilities as well; for example, it can shoot Phazon beams reminiscent of Samus's Power Beam, as well as hover, recover health, and create shadow clones called "Dark Echos".

Samus first meets her doppelgänger near the beginning of Metroid Prime 2: Echoes. Dark Samus destroys a light crystal beside Samus, inciting a horde of Ing creatures to attack Samus whilst vulnerable in the toxic Dark Aether atmosphere. The encounter leaves Samus without the possession of many of her power-ups, leading the player to solve puzzles and defeat enemies in order to reclaim them.

The player encounters Dark Samus three times in the game, with each battle featuring a stronger version of the adversary. The conflict between the two combatants spans over several regions of two dimensions, ultimately culminating with a final fight before the destruction of Dark Aether, during which Dark Samus changes several times between her third and fourth forms. Samus defeats her decaying counterpart, leaving Dark Samus to seemingly perish within Aether’s dying dimension. However, an unlockable cinematic reveals Dark Samus reforming in a cloud of Phazon after the game’s conclusion. According to a logbook scan, Dark Samus can perform this reforming ability from any type of destruction short of 'total atomic disruption'.

Dark Samus' final appearance occurs in Metroid Prime 3: Corruption. In Corruption, the Space pirates move to collect a sample of Phazon from what remains on planet Aether. In their hurry to collect as much as they can before the Federation, a group of Space Pirates accidentally bring Dark Samus aboard their ship, who had been revitalized amongst the Phazon supply. According to in-game logs, Dark Samus escapes from the cargo hold and quickly wipes out a third of the Pirate crew, the remainder of whom submit to her as their new leader.

Dark Samus then orders the Pirates to steal one of the Aurora Units, the Galactic Federation's organic supercomputers, which she subsequently uses to spread Phazon corruption on a galactic scale. In their efforts to stop her, Samus and three other Bounty Hunters end up corrupted with Phazon by her. After recovering from her attack, Samus is informed that the pirates were corrupting entire planets with Phazon Seeds, known as "Leviathans". After defeating each one of the other hunters, who had fallen under Dark Samus's control due to their Phazon corruption, and neutralizing each one of the Leviathans planted by her, Samus confronts her nemesis at the very source of the Phazon itself, the planet Phaaze. By using the same energy generated by her corrupted body to fight and destroy Dark Samus presumably for good, Samus manages to render all of the Phazon generated by the planet inactive, freeing her body from the corruption and triggering a chain reaction that culminates in the planet's explosion.