Black Manta had the Flyer docked in a cave near Atabey's Shrine, and imprisoned Aquaman in his base. The Flyer was being refueled by energy generators.
Just as Manta and Luthor were about to escape, Aqualad and Alpha Squad intervened. Though it was being recharged, the Flyer's weapons systems were still functioning. Nonetheless, Alpha Squad managed to take out the main guns by overloading the generators.
After the Justice League and the Team had found their location, the Partner placed a bomb on the island. Manta ordered his troops to escape in the Manta-Flyer. He jumped in the water after a confrontation with his old friends and hitched a ride on the roof.
The Manta-Flyer dropped a special weapons platform off the coast of Cape Canaveral, and then retreated to a safe distance. Kaldur'ahm ordered the captured Lagoon Boy to be taken to the Flyer. After the mission was fulfilled, Kaldur and his troops escaped in the vessel.
After Blue Beetle and Impulse escaped their attackers, the strike team headed to the skies again. Kaldur had "given" Impulse a tracker, which allowed them access to Mount Justice. The Manta-Flyer submerged off the coast of the mountain, and moored on the beach. After their raid, they took their prisoners Blue Beetle, Impulse and Beast Boy aboard the ship, and detonated a bomb Kaldur'ahm had planted in the Cave.
Deathstroke and Tigress took the Flyer to Chicago, where they waylaid and captured Miss Martian. Deathstroke was later assigned to the Flyer full-time, where he would monitor Miss Martian's progress with curing Aqualad, and was tasked to detonate the explosives in the collar suppressing her other powers should she refuse to cooperate. To protect himself from her influence, he piloted the Flyer a safe distance from the Sub—far enough from the Martian's telepathic reach.
Deathstroke continued to monitor Aqualad's progress. A rock formation that temporarily obscured his view allowed Sportsmaster and Cheshire to board the Manta-Sub unnoticed. When the fiends wreaked havoc in the sub, Deathstroke was forced to bring the Flyer in so he could intervene.