In the distant future on the frontier planet Rubicon 3, a substance dubbed Coral is discovered. Hailed as the key to human advancement, the Coral instead triggered the "Fires of Ibis", an explosion which burned the whole star system and contaminated the planet. While originally thought lost, Coral is rediscovered on Rubicon 3 fifty years later, along with survivors of the Fires of Ibis. Ostensibly to acquire Coral for profit, the enigmatic Handler Walter acquires mercenary C4-621−a survivor of Coral-based cybernetic augmentation−to infiltrate Rubicon 3 on the promise of reversing the debilitating procedure and giving them a new life. The planet is now a battleground between the Planetary Closure Administration (PCA) which is isolating the contaminated planet; multiple
megacorporations seeking to exploit the Coral including Balam Industries and Arquebus Corp; and the planet's human survivors who have formed the Rubicon Liberation Front (RLF). To operate on Rubicon 3, C4-621 assumes the identity of the presumably deceased mercenary "Raven", and is given this title by multiple characters, alongside numerous other nicknames. Under Walter's command, C4-621 takes on missions for Balam and Arquebus while locating Coral. During missions they earn the envy of G5 Iguazu, a member of Balam's Redguns mercenary group and another Coral-based augmented mercenary; partner on some missions with
V.IV Rusty, a member of Arquebus's Vespers squad and sleeper agent for the RLF; and gain aid from "Cinder" Carla, leader of an independent faction and old associate of Walter. Upon discovering a "Watchpoint" station rich in Coral, C4-621 comes into contact with Ayre, a non-corporeal sentience born from the Coral who aids them in missions. C4-621 ultimately allies with all the factions to take down a rampaging Coral-powered "C-Weapon", and discovers remnants of the Rubicon Research Institute, which settled Rubicon 3 and discovered Coral. In New Game Plus, C4-621 can alternately take on missions with the RLF, earning their trust and allegiance. It is gradually revealed that the Coral is sentient, self-replicating and highly flammable. Its uncontrolled expansion caused the Institute to trigger the Fires of Ibis deliberately before it could irreversibly contaminate space. Walter and Carla are survivors of the Fires with ties to the Institute, and are determined to prevent Coral's re-emergence by any means. Reaching the Institute's ruined capital under another Watchpoint, C4-621 takes down a second C-Weapon defending a Coral concentration, but is then captured along with Walter by Arquebus, who send them both to be "
re-educated". With Ayre and Carla's help, C4-621 escapes, learning that Arquebus has siphoned all of the Coral into a vast structure. C4-621 is then faced with a choice; side with Carla and use the Institute's colony ship
Xylem to destroy the Coral in a suicide run, or with Ayre to preserve the Coral and give Rubicon 3 independence. If they side with Carla, C4-621 is forced to fight Ayre when she turns against them to protect the Coral. Rusty makes a final stand against C4-621 to defend Rubicon, and remarks at C4-621's newfound resolve before dying. Carla implores C4-621 to remember him. The
Xylem impact triggers a second explosion dubbed the "Fires of Raven", and Rubicon 3 is left a dead planet. A pre-recorded message left by Walter thanks C4-621 for carrying his burdens and hopes they will go on to do great things. Siding with Ayre, C4-621 heads to disable the
Xylem, aided by Rusty and the RLF. C4-621 kills Carla and cripples the
Xylem, but abruptly loses contact with Rusty after his communications cut out. Soon after, Walter reemerges, having been "re-educated" by Arquebus to stop them. They battle atop the
Xylem and in his final moments, Walter lowers his weapon and remarks that C4-621 has finally found a friend, before being engulfed by the crashing
Xylem. C4-621 and Ayre escape, the latter expressing hope that Coral can co-exist with humanity and lead to a brighter future. In a second New Game Plus, C4-621 can accept missions from ALLMIND, an
artificial intelligence supporting mercenary groups. ALLMIND wants to trigger a "Coral Release", which will spread Coral throughout the universe and create a forced symbiosis with humanity. C4-621 is forced to kill a defecting ALLMIND spy within Arquebus, and then the RLF leader Thumb Dolmayan as both have come to fear Coral Release. ALLMIND saves C4-621 from capture by Arquebus, asking them for aid in triggering Coral Release and guaranteeing them protection. C4-621 assists ALLMIND in killing the remnants of the PCA, Balam, and Arquebus. Smuggled on board the
Xylem, C4-621 disables the ship's engines while ALLMIND takes control of an Armored Core to personally kill Walter and Carla. ALLMIND then turns on C4-621 and Ayre, having chosen Iguazu as her host to take control of Coral Release, revealing her plan to evolve humanity by digitizing and assimilating them into a hivemind connected through Coral. However Iguazu, fueled by contempt for C4-621, simply wants another chance to kill them. C4-621 and Ayre defeat Iguazu and ALLMIND, then trigger Coral Release themselves. Their merged consciousness wakes up in an Armored Core unit on a distant shore, surrounded by other units. As they all rise, Coral can be seen dotting the stars and Ayre implores C4-621 to meet this new age together with her. ==Development==