In 2552, the United Nations Space Command suffered a catastrophic defeat in the Fall of Reach; with humanity's single greatest stronghold lost, the Covenant advance towards Earth now appeared unstoppable. With the majority of the Spartans apparently killed on Reach during preparations for Operation: RED FLAG, the members of Gray Team stood as the only available members for what was to be a devastating counterattack against the Covenant as revenge for the billions already lost to the war. Gray Team was selected to launch a covert penetration of Covenant space, with the goal of eliminating as many of the Covenant military's Sangheili leaders as possible and to target one of their worlds for destruction via a NOVA bomb. The three members of Gray Team, Jai-006, Adriana-111, and Mike-120 departed for their mission aboard the prowler UNSC Vacuna.
The Vacuna ferried its elite team into deep space, facing numerous communications blackouts with the UNSC as they sought out their primary objectives. Finally, word arrived that the Covenant had found and invaded Earth. ONI initiated Operation Endgame, clearing Gray Team to deploy the NOVA bomb at their earliest disposal before losing contact. Gray Team sought to use the bomb on Sanghelios, but decided against it as the planet was too heavily defended. Gray Team found another candidate; the nearby colony world of Glyke, home to billions of Sangheili citizens. The team unanimously voted Glyke as their target, departing to the surface of the planet in December of that year.
Upon touchdown, Gray Team readied the NOVA bomb for detonation, and with the countdown initiated retreated back to the Vacuna for immediate departure. The subsequent explosion completely annihilated the planet and all life upon its surface, damaging the Vacuna as it attempted to clear the destruction. Unable to save the vessel, Gray Team was forced to evacuate aboard the prowler's single Class-5 Bumblebee escape pod, codenamed Whiskey Tango Foxtrot One. The three members of Gray Team were the only survivors of the Vacuna as the crippled prowler was destroyed, and the Spartans were left stranded in space with no way to contact the UNSC. Having retrieved several cryo chambers before escape, the Spartans entered cryo-sleep as they awaited rescue.
Unbeknownst to Gray Team, the war had ended in a human victory due to the outbreak of the Great Schism, leading to the Sangheili-UNSC alliance that saw the complete destruction of the Covenant at the Battle of Installation 00. An unsteady peace was formalized between the two races by the time of Glyke's destruction.
Gray Team was presumably listed as MIA as was the tradition with all Spartan-II supersoldiers throughout the War, and were among the few Spartans to truly be so. Gray Team's lifeboat drifted through space for six years until 2558, when the Sangheili warship Unwavering Discipline recovered it and imprisoned the Spartans while they remained in cryo-sleep. The vessel's Fleetmaster, Rojka 'Kaasan sought to bargain the Spartans' freedom with the UNSC as part of his revenge for those killed on Glyke.
In an effort to get Gray Team back, ONI had Melody Azikiwe negotiate with Rojka while secretly trying to find a way to wake them up herself. After Thars 'Sarov attacked Rojka, Melody managed to awaken Gray Team from cryo and they stole back their lifeboat and escaped to the surface of Carrow where Gray Team got caught up in the massive Carrow Conflict. After the battle, ONI offered a deal where Gray Team would join a joint interspecies team with part of the deal being that Thel 'Vadam, the leader of the Swords of Sanghelios, would grant them a formal pardon for their actions. Gray Team ultimately took the deal with a list of demands attached. Additionally, after fighting side-by-side with Gray Team in the battle, Rojka let go of his vengeance upon them.
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