Option Two is the nineteenth episode of the fifth season of the television series Agents of S.H.I.E.L.D., and the one-hundred and seventh episode overall.
Coulson and the team find themselves under siege at the Lighthouse.
As S.H.I.E.L.D. discuss the aftermath of the Infiltration into the HYDRA Herefordshire Facility and the attempted kidnapping of Robin Hinton, an argument erupts between the different agents: notably, Daisy Johnson blames Yo-Yo Rodriguez for killing Ruby Hale instead of taking her prisoner, although Rodriguez insists she made the right choice. Phil Coulson ends the argument and orders everyone to get back to their jobs so S.H.I.E.L.D. can upgrade the Zephyr One and use it to send the Gravitonium into the Sun to destroy the dangerous element. They also decide to enlist Tony Caine's assistance for taking care of Carl Creel, Robin and Polly Hinton.
Johnson is tasked with delivering Creel and the Hintons to Caine. However, she and Melinda May actually pursue another agenda: they asked Caine to investigate the Project Deathlok to find something which could help Coulson with his condition, although he forbade such initiatives. Johnson leaves and May assures her that she will cover for her in the Lighthouse.
As Leo Fitz, Jemma Simmons and Deke Shaw prepare the Gravitonium for transfer, Glenn Talbot calls for Coulson in his cell. Talbot explains that non only did he attempted to kidnap Robin, but he also activated the Lighthouse's landing assist system, enabling outsiders to find the S.H.I.E.L.D. secret base. Indeed, the Confederacy led by Qovas soon brings a gigantic spaceship to the Lighthouse. Via video communication, Qovas demands the Gravitonium to be handed over, but Coulson, who accidentally triggered the base's lockdown for fifteen years according to the nuclear attack protocols, firmly refuses, prompting Qovas to end the negociations.
Rodriguez attempts to make up with Alphonso Mackenzie, claiming that she only did what she did to protect the world, with Mackenzie and herself within. However, this quickly turns into an argument over what Rodriguez did and what happened to her arms. Rodriguez again tells Mackenzie that she loves him and that they will figure this out, but Mackenzie is not so sure, leaving Rodriguez puzzled. Rodriguez then talks with May, who tries to advise her on the way to cope with her actions.
As Coulson notices that he can neither reach Johnson nor receive any message from her, May reveals Johnson's actual purpose. Upon learning that Johnson and May are trying to save Coulson at all cost, she feels desperate as her future self precisely told that this kind of actions would eventually doom the world. May counters that by saying that in the future, Robin told that Coulson would "bring the pieces back together", meaning that S.H.I.E.L.D. needs Coulson alive. However, the argument is ended as Coulson figures out that the base's lockdown will not stop their invaders.
Indeed, Qovas sends a battalion of Remorath through the Phase Harmonic Teleportation Device, which enables them to directly teleport inside the Lighthouse. The Remorath begin to kill several S.H.I.E.L.D. agents and Shaw barely escapes. He joins the control room and explains to his friends what are the Remorath's capabilities. Upon facing such danger, Coulson decides to evacuate the Lighthouse with the Zephyr One. Fitz decides to find an override system to lift the lockdown while Simmons secures the Gravitonium and Rodriguez leaves to find Talbot.
Rodriguez finds a confused Talbot in his cell. She handcuffs him and proceeds to escort him through the Lighthouse. However, they encounter more Remorath and are forced to retreat in the labs with Simmons, Davis and Piper. Meanwhile, Fitz and Wahl are also confronted by the invaders. Wahl is killed, but Fitz is rescued by Shaw. However, Fitz and Shaw discover that the override system has been destroyed by the Remorath, preventing S.H.I.E.L.D.'s escape. Shaw and Fitz then make it back to the control room with Mackenzie.
S.H.I.E.L.D. faces the Remorath in two different spots. Coulson, May, Fitz, Mackenzie and Shaw barely withstand the assault in the control room while Rodriguez, Davis and Piper try to keep the Remorath from reclaiming the Gravitonium. In the labs, Talbot finds the Particle Infusion Chamber and decides to use it to make up for his past actions. He incapacitates Simmons and reactivates the Gravitonium infusion process, gaining the same gravity manipulation abilities than Ruby's. Using these new powers, Talbot easily crushes the Remorath throughout the Lighthouse, ending the battle. He then takes Coulson with him up in the air on a concrete chunk so they can exit the Lighthouse.
Meanwhile, Johnson meets with Caine, who explains everything he found about the Deathlok Program. He gives her a Centipede Device and mentions John Garrett's history, but he also says that there is an unidentified ingredient in the Centipede Serum, and that he cannot find the place where this ingredient was found. Reading the documents that Caine provided her with, Johnson states that they are not looking for a place. She leaves Caine and retrieves the grave of her mother Jiaying before starting to dig in it.