The Raid of the Guest House was a forced attempt at obtaining medical assistance from a secret facility in order to save Skye's life, met with resistance from the security personnel inside.
Leo Fitz and Jemma Simmons were ordered to study the Clearance Level 10 file regarding Coulson's death and recovery to learn about the actual procedures used, and to choose one that could save Skye upon arriving to Bethesda, the location where Coulson was supposedly treated after his death. However, Fitz and Simmons tried to contact Dr. Streiten, knowing that he was one of those responsible of the procedures, but the crew of the trauma center in Bethesda informed them that Streiten had gone off the grid, and the personnel and facilities that appeared in the file did not exist, at least in Bethesda.
Phil Coulson prepared to raid the compound if necessary with John Garrett's help, who was on the Bus to take custody of Ian Quinn. Coulson ordered Grant Ward to accompany them, and also wanted Leo Fitz's assistance in case the medical crew or the facility were damaged, to determine the equipment Jemma Simmons would need to help Skye. Simmons and Antoine Triplett stayed in the Bus, preparing Skye to be moved to the facility to be operated on, and Melinda May also stayed behind in case they needed to escape the area inside the Bus.
Coulson, Ward, Fitz and Garrett approached the gates of the compound. The two security guards stationed at the compound, Alpha and Beta, were surprised to see someone coming, as there were no visits scheduled for a couple of weeks. The guards used their protocol, but since Coulson did not know the countersign and it was not found in any of S.H.I.E.L.D.'s directive protocols, he could not answer. Coulson tried to reason with the people inside, letting them know that a member of his team was in dire need of medical assistance, but they did not respond, forcing Coulson and his team to attack the base.
Ward shot at the security camera located at the gates of the compound, and Fitz started to hack the gates, quickly gaining access to the compound. Alpha and Beta prepared to defend the Guest House, praising the agents' skills as having been able to hack their way in, but since they did not know the countersign, they could not let them pass.
Coulson and his men descended through an elevator, and noticed that the personnel of the compound set an ambush for them. The communications with the Bus were not functioning as they were at great depth inside the compound, and the team advanced until Fitz was able to breach a bulletproof glass door.
Once they entered the room, a firefight occurred between the S.H.I.E.L.D. agents and the guards. Coulson tried to negotiate again with the guards, but they did not cease firing, so the agents were forced to defend themselves. Ward and Garrett were able to clear the path, killing Beta and wounding Alpha.
Coulson and Ward followed the blood trail of the wounded guard, and when they found him, Coulson asked him about the doctors stationed at the facility. However, the guard revealed that the medical staff did not stay inside the compound, so it was empty. Alpha seemingly recognized Coulson from his days at the Guest House and, before dying, revealed the existence of a timer of a bomb set in case of infiltration.
Garrett located a large amount of Semtex all over the compound, and Fitz was unable to hack the panel to reopen the bulletproof doors before the explosives destroyed the whole mountain. Coulson asked Garrett and Ward to disarm the explosives or at least find a way to escape while Coulson and Fitz went to find the GH.325 drug. While looking for it, Coulson found the room where he was operated on, seeing the machine used to rewrite his memories.
Ward and Garrett were unable to deactivate the bomb, as they had not enough time to locate the detonator in the entire compound, so they decided to use some Semtex to blast the door.
Coulson and Fitz entered a room marked with a Biohazard Containment sign filled with different chemical compounds, and managed to locate different vials with drugs marked with the GH letters, including the GH.325. Ward arrived to inform them that they couldn't stop the bomb. Coulson ordered Fitz and Ward to get the drug to Simmons, but he stayed behind to check a vault marked with the acronym T.A.H.I.T.I.
Inside the vault, Coulson saw a machine where the different GH drugs were being synthesized, with a series of conduits that led to a chamber, the seeming origin of the drugs, marked with the initials G.H. As Coulson opened the chamber, he discovered that it housed the corpse of a blue alien whose bodily fluids were being harvested to create the drugs.
Garrett was able to open the door using a small explosive taken from the walls, and told Fitz and Ward to make sure Skye received the drug while he went to find Coulson. As Fitz approached the Bus, he communicated with the agents staying inside to take the plane off the ground to avoid the impending collapse caused by the explosion.
Garrett found Coulson wandering the facility in shock, and listened as he suddenly started to shout that they could not give the drug to Skye. Garrett convinced Coulson to leave before the facility exploded and the whole mountain collapsed.
Despite Phil Coulson's warnings, Jemma Simmons had no choice but to administer the GH.325 drug to Skye, as she was dying. Within a short time of receiving the drug, Skye had stabilized and began to recover. Coulson, however, was worried about her and continually watched her for any side effects of the drug, though she did not display any.
Unbeknownst to everybody, John Garrett was able to take many vials, all marked with the prefix GH, in order to continue his work in an attempt to reverse-engineer the drug that resurrected Coulson.