Following the formation of the New Republic, Green Squadron's starfighters escorted a convoy led by the GR-75 medium transport Dewback's Burden to Bhuna Sound, where they were ambushed by pirate TIE interceptors. "Green Leader", a B-wing starfighter pilot, was destroyed with the rest of the convoy.
During the selection period for what would become Wraith Squadron, candidates including Kell Tainer and Hohass Ekwesh used the designation of Green Squadron in simulated combat missions.
The active Green Squadron, a Y-wing bomber squadron, was sent from Borleias by General Horton Salm to participate in an ambush of the Warlord Zsinj-aligned Imperial-class Star Destroyer Implacable over Ession. Along with Rogue and Blue Squadrons, Green Squadron passed through the system's security aboard the Super Transport VI Red Feathers, launching from the ancient container ship as it broke up in the planet's gravity.
Following the fall of Coruscant in 10 ABY, the squadron's leader and a rookie wingmate performed a patrol mission in the Cyax system over the New Republic's Pinnacle Base, where they encountered a target which did not broadcast any ID codes. As "Green Leader" and "Green Three" moved to intercept, the commander of the vessel, New Republic Admiral Ackbar, identified it as the flagship Defiance and explained that his ship had received damage to its transponder after encountering an Imperial convoy during a reconnaissance mission to the Galactic Core. At Ackbar's request, "Green Leader" relayed his message to Republic leader Mon Mothma.
Working once again with Blue Squadron, Green Squadron was dispatched by Ackbar to cover the evacuation of Calamari. Now a mixed group of B-wing, Y-wing, and X-wing pilots, Green Squadron deployed from the New Republic Star Destroyer Emancipator and targeted the Imperial World Devastators assaulting the planet, losing their squadron leader to a TIE/D automated starfighter in the ensuing battle.
Later in the reign of the reborn Emperor Palpatine, a Green Squadron of X-wing starfighters led by another "Green Leader" was in the process of boarding the troopship Pelagia when a projectile from the Emperor's Galaxy Gun superweapon was detected on approach. Green Squadron deployed to counter the missile, but were unable to penetrate its shielding and were destroyed, along with the Pelagia.
In the Battle of Coruscant and Battle of Borleias in the Yuuzhan Vong War, it consisted of E-wings and served under Captain Yakown Reth. Squadron members including Reth were reformed into Blackmoon Squadron.
During the Battle of Coruscant, Green Squadron initially covered the Pride of Honor, a New Republic capital ship. However, a senator ordered the squadron to protect his ship instead, resulting in extensive damage to the Pride of Honor. The Pride of Honor was scrapped after the battle due to the damage it sustained.
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