All characters and craft are introduced in game release order. Spoilers, marked and unmarked, ahead!
Debuted in Kamui
ALLTYNEX OSThe general-purpose administrative Master Computer built by humanity. It going rogue and using its control over a huge automated army to attack humankind is what causes the game's plot. Although ALLTYNEX itself is destroyed at the end of the first game, a Neural Network based on its OS and using the uploaded minds of hundreds of humans is created in RefleX to command the forces of the Mechanized Temple against the Raiwat, effectively resulting in the AI's rebirth. This same Neural Network is used in Kamui by Xaffiquel to subvert humanity's forces against them.
Xaffiquel de AliceThe scientist who developed Brain Fusion Theory. His research on the matter led his colleagues and the public to dismiss and ridicule him, but he was later recruited by a secret organization who helped him acquire test subjects...one of which was has daughter Panaffil.
Panaffil de AliceXaffiquel's daughter, and the protagonist of Kamui. Her mind is uploaded into Kamui unit #2. Unlike the other test subjects, she retained her consciousness during the Brain Fusion process, and as such her unit is the only one to retain the original mind of its subject.
KAMUIA class of fighter that is piloted by a psychic's brain. Its armaments usually consist of a standard energy blaster, lock-on lightning attacks, and a Lightning Blade attack. Kamui #2 is piloted by Panaffil de Alice. In addition, a squadron of mass-produced Kamui units are seen in KAMUI stage 4, with altered weapons. In RefleX, two Kamui units are dispatched to eliminate ZODIAC units Ophiuchus and Libra.
Debuted in RefleX
Guehala DennisThe developer of the Phoenix in RefleX and the pilot of the Armed Saboteur and the protagonist in ALLTYNEX Second. Following the battles with ALLTYNEX and Satariel, he is transported 200 years into the future, where he hinds out the horrible truth about the Senate and ALLTYNEX. Joining the anti-government group Valkyness, he goes on to develop their signature Serpent fighters, as well as the MK-II Phoenix, using ZODIAC Ophiuchus's core as a source of energy. Dennis is killed at the very beginning of RefleX, along with the rest of the crew on the carrier Ophiuchus.
ALFI-PH2RX Phoenix 02 / ZODIAC Ophiuchus(Not to be confused with the carrier Ophiuchus.) A general-purpose fighter craft, piloted by the unnamed protagonist. Alongside its standard-issue energy blasters, it is equipped with a shield system capable of reflecting some attacks while nullifying others. It is carrying the core of ZODIAC Ophiuchus, which is used to help generate the shield. ZODIAC Virgo totals it in Area 7, killing the pilot. This triggers the transformation of the Phoenix into Ophiuchus, awakening the A.I., which is programmed to destroy the other ZODIAC units, Virgo included, at all costs, even going as far as to cause massive collateral damage to the Earth in the process.
Global Unified Army
Virgo — Pilot: Spica Astrea(Not to be confused with ZODIAC Virgo.) The first of the pseudo-ZODIAC units the player encounters. It makes its introduction by nuking the carrier Ophiuchus, killing everyone on board, including Doctor Dennis, with the Phoenix narrowly escaping, and then engaging the Phoenix in combat, only to be defeated and retreat. Virgo reappears in Area 6, this time allied with Valkyness, briefly seen pursuing ZODIAC Virgo. It then accompanies the Phoenix in Area 7 to the ALLTYNEX ruins, only to be destroyed by ZODIAC Virgo. Spica managed to escape with her life, joining the Gehenna Church afterwards.
A race of anthromorphic creatures. Centuries ago, the Raiwat constructed the ZODIAC units and their power to establish empric rule, but one day the ZODIAC units went berserk and Turned Against Their Masters. The Yuda Clan constructed an anti-ZODIAC weapon, the ZODIAC Ophiuchus, and then fled the homeworld for Earth, resulting in catastrophic destruction of Raiwat civilzation. As the Raiwat took centuries to rebuild their civilization, their genes mutated to adapt to the scorched environment, causing them to mutate into beastly creatures. Now, the Raiwat are out to get revenge on the descendents of the Yuda, taking back control of the ZODIAC weapons to unleash destruction on the Earth.
TsukikagerouCommander-in-chief of the Raiwat Drone Invasion Force, and the military head of their attack on Earth.
The ZODIAC units
ZODIAC VirgoThe first of the ZODIAC units to reach the Solar System. It is first seen in Area 4, finishing off Cancer, whose destruction ends up destroying the Valkyness base as well. It reappears briefly in Area 6, being chased by the pseudo-ZODIAC Virgo, and again in Area 7, where it makes short work of Virgo, and soon after blows out the Phoenix, murdering its pilot...only to be destroyed by its energy-winged ZODIAC form.
ZODIAC LibraThe last of the ZODIAC units to be seen, after the destruction of the other eleven.
Debuted in ALLTYNEX Second
SatarielA mysterious machine drawn out of the Qliphoth by Alltynex after it's destruction.