The Infiltration into Qovas' Ship was a rescue mission planned by S.H.I.E.L.D. in order to save Phil Coulson and Glenn Talbot from the Confederacy. After being betrayed by Talbot, it turned into an escape mission, where they would destroy the ship.
In order to acquire the Gravitonium which had been promised by HYDRA but had been confiscated by S.H.I.E.L.D., the extraterrestrial alliance known as the Confederacy led a siege on the Lighthouse under the supervision of the Remorath Qovas. A battalion of Remorath invaded the Lighthouse, but in the end, they were all defeated by Glenn Talbot, who had infused himself with the Gravitonium and thus gained gravity manipulation abilities.
Using these newfound powers, Talbot took himself and Phil Coulson into Qovas' Ship so they would confront Qovas face to face and force him to end his assault on Earth. As they figured out that they could need backup, S.H.I.E.L.D. Agents Melinda May and Quake decided to infiltrate the ship as well to rescue Coulson and Talbot and bring them back to the Lighthouse. Unbeknownst to them, however, Talbot had become mad with power and, upon being convinced by Taryan to find more Gravitonium, he turned on S.H.I.E.L.D. and decided to side with the Confederacy.
Using a newly upgraded Zephyr One which had been modified so it could be taken into space, a S.H.I.E.L.D. team led by Melinda May and Quake and notably comprised of Davis, Kim and Deke Shaw left the Lighthouse to reach Qovas' Ship which had flown away outside the atmosphere. Once the vertical propulsion took them into space, the team activated the plane's cloaking, enabling them to stealthily dock to the Remorath spaceship. At this point, the Remorath spotted them and reported the event to Qovas. This angered Glenn Talbot, who ordered the Remorath to capture the intruders.
Quake and May made their way through the spaceship and were quickly confronted by Talbot, who threatened to kill Phil Coulson if they did not surrender. Quake and May did not understand the situation but Quake, in an attempt to defuse it, suggested that she would willingly stop to fight if Talbot let Coulson go. Hale, who was present as well, claimed that she trusted Quake, much to Talbot's surprise. When Hale explained that Quake had tried to help her daughter Ruby Hale, Talbot insulted the latter. Hale then attempted to retake control by using the Faustus method, but her attempt failed and she was murdered by Talbot.
Upon seeing that Talbot had truly turned on them, Quake attempted to attack him. However, he appeared to be incredibly resilient towards her powers. Talbot then used his own powers to knock Quake unconscious. As May aimed her gun at him, Talbot ordered her to surrender if she wanted to pare the lives of her friends. May reluctantly complied and dropped her weapon. Talbot then instructed Qovas to take the S.H.I.E.L.D. agents as prisoners of war.
While the still unconscious Quake was subjected to an Astralscope illusion so she could have a conversation with the Kree Taryan who wanted her as a disciple, Qovas locked up Coulson and May in a cell. Left alone, they discussed the fate of Talbot and agreed on the fact that they had to get out and do their possible to reason and stop him. Meanwhile, Talbot himself left the ship, infiltrating into the Zephyr One where he murdered Kim while Shaw and Davis hid in horror. Talbot, along with two Remorath soldiers, stole the plane's Quinjet to return to Earth and Shaw reported the attack to Alphonso Mackenzie in the Lighthouse.
Using his prosthetic hand, Coulson located a way of escaping. As he and May opened the door of their cell, Shaw killed the guard, having infiltrated the spaceship to rescue them. The three of them then attempted to find an exit. As they made their way through the corridors, they encountered a couple of Remorath soldiers, who were taken down by Quake, who had broke free of her illusion and dispatched her own captors. The S.H.I.E.L.D. team then agreed that they could not leave the spaceship before changing the target of the Ionizer Missiles Qovas had aimed at the Lighthouse.
May suggested that she would remain with Shaw, as she needed her knowledge of the Confederacy's language to change the targets, while Coulson and Quake would escape with the Zephyr One. Coulson refused, preferring that they remained all together. As they argued, more Remorath arrived and began shooting at them. Coulson protected May behind his Energy Shield and the two shared a passionate first kiss, much to Quake's and Shaw's surprise, who dispatched the last opponent. Coulson then agreed to May's plans and left for the Zephyr One with Quake.
Arriving in the plane, Coulson and Quake realized that Remorath had infiltrated it as well. Fearing to lose Davis in the fight and thus not being able to return on Earth, Coulson and Quake fought across the plane and successfully defeated the Remorath, enabling them to safely leave. However, the intensity of the fight deepened Coulson's weakened condition and he fell unconscious.
Meanwhile, May and Shaw soon arrived in the spaceship's control room, taking down the two warriors guarding it. As Shaw worked on changing the target, May extracted the fallen soldiers razor claws right before Qovas himself arrived to kill them. A furious duel erupted between May and Qovas while Shaw correctly set up the ship's Phase Harmonic Teleportation Device so he and May could return to the Lighthouse. In the end, although Qovas was partly able to disarm May, he grew wary of her resistance and launched the missiles himself.
However, May and Shaw then revealed what they had done and rushed to the teleportation device. As they teleported away, Qovas watched the Ionizer Missiles being fired and then changing their course to hit Qovas' own spaceship, resulting in the destruction of the ship and Qovas' death.
Despite being destroyed, the remnants of Qovas' ship were reclaimed by Talbot, who used it to transport himself as well as Polly and Robin Hinton into Chicago, where he would soon battle against S.H.I.E.L.D..