S.O.S Part One is the first episode of the two-part season finale of the second season of Agents of S.H.I.E.L.D. and the forty-third episode overall. It premiered before S.O.S. Part Two, both being aired as a single block.
S.H.I.E.L.D. puts everything on the line to survive a war that blurs the line between friend and foe. Coulson and his team will be forced to make shocking sacrifices that will leave their relationships and their world changed forever.
As Jiaying staggers outside of her office and collapses due to blood loss from her self-inflicted gunshot wounds, Skye, Jemma Simmons and Lincoln Campbell rush to her side. Jiaying lies to the three and tells them that Agent Robert Gonzales had said to her that Inhumans should be exterminated before shooting her. Skye prepares to find Gonzales, but Jiaying asks her to stay by her side and assures her that Gordon will take care of him before telling Lincoln to evacuate the other Inhumans to safety. Simmons offers to look at Jiaying's wounds, but Jiaying tells her that S.H.I.E.L.D. has done enough, so Skye advises Simmons to leave with the other agents while she stays with her mother. Jiaying then nods to Gordon and another Inhuman who proceed to carry out her plan.
Meanwhile, on her Quinjet, Agent Melinda May speaks with S.H.I.E.L.D. director Phil Coulson and Agents Leo Fitz and Lance Hunter, who are at the Playground, asking if they were able to make any contact with Agent Bobbi Morse, as her quinjet has not arrived nor has she been making any contact with May. Hunter, Bobbi's ex-husband, quickly leaves to try and find Bobbi, while Coulson asks how Skye is. May replies that Skye was disappointed that he was not the one meeting with Jiaying. Simmons then arrives back on the quinjet to inform everyone about the supposed situation, but when Coulson asks where Gonzales is, Simmons admits that she does not know. Fitz remarks that Gonzales got what he wanted by attacking the Inhumans, but Coulson points out that Gonzales would not do that and suspects that something else is happening. Not wanting to escalate the situation until he knows what is going on, Coulson tells May to find Gonzales and get the other agents out of Afterlife. May goes to find Gonzales, telling the other agents on her quinjet to make sure all three quinjets are ready to depart when she returns. Suspecting Calvin Zabo's involvement, she tells the other agents to make sure he is secured. On one of the other quinjets, an agent carrying the device that tracks Gordon's teleportation tells his partner that Gordon is moving. At that point, Gordon and the other Inhuman arrive on the plane. The Inhuman quickly disables one of the agents, while Gordon teleports with the other off the quinjet. The Inhuman then destroys the tracking device and starts piloting the quinjet.
After Lincoln has taken the other Inhumans to safety, he arrives to help Skye take Jiaying to a doctor. At that point, the quinjet piloted by the Inhuman fires missiles at buildings in Afterlife. Manipulating Skye, Jiaying asks why Skye would allow this to happen. Skye swears that she was not responsible for this. At that point, Alisha Whitley arrives and, along with Lincoln, takes Jiaying to a doctor. After seeing an Inhuman shot down by an agent, an enraged Skye uses her powers to disarm the agent of his gun and proceeds to beat the agent unconscious until May arrives and tells Skye to stop. Skye demands to know what S.H.I.E.L.D. has done, and May explains that she and the other agents are trying to find out the same thing but tells Skye to stand down. Angered that May would tell her to stand down after what Gonzales supposedly had done, Skye says that May needs to be the one to stand down. May asks where Gonzales is and says that they can fix the situation, but Skye says that it is too late and that May and her agents need to leave. May replies that she needs to find Gonzales first. Skye proceeds to fight May, forcing May to reluctantly fight back. May tells Skye that she does not want to hurt Skye, but Skye tells her that she will not, and the two continue fighting. Ultimately, May demands that Skye help her solve the problem, but Skye tells May that she is no longer welcome in Afterlife and uses her powers to knock May unconscious.
On the Iliad, Agent Alphonso Mackenzie, having just resigned from S.H.I.E.L.D., is gathering his things and talks with Agent Oliver about his future plans when an alarm then rings throughout the ship, ordering agents to report to their stations, and Mack and Oliver learn of Gonzales's death.
Meanwhile, May awakens on her quinjet to hear Zabo listening to music and singing. Coulson asks Simmons if they know who fired the missiles, but Simmons replies that they still do not know while May demands to know where Skye is. Simmons blames Gonzales for starting the war, but Agent Anne Weaver claims that Gonzales would never do something like this, but Simmons reminds Weaver that Gonzales had led an unprovoked attack on the Playground. Weaver explains that Gonzales would not have done this, revealing that Gonzales had had Weaver go to great lengths to get Jiaying a gift as a peace offering. Coulson agrees that Gonzales was too smart to do something this sloppy. Weaver recommends that they attack the Inhumans, but Coulson insists that he will not start a war until he understands the situation and orders Weaver to take command of the Iliad. He then tells May and Simmons that he does not believe that Skye would turn against them, but May recounts her recent fight with Skye, but Coulson attributes this to her confusion after the shooting of her mother. Coulson decides that they can try to get information from Cal.
Back at Afterlife, Skye, Campbell, and Whitley watch Jiaying get treated by a doctor, and Skye offers to donate blood to help her mother, but Lincoln angrily tells her that she has done enough and proceeds to blame Skye for convincing Jiaying to trust S.H.I.E.L.D., despite her misgivings. Jiaying defends Skye and takes the blame for trusting S.H.I.E.L.D. and tells Lincoln that Skye probably feels just as betrayed as the other Inhumans do, if not more. However, Skye expresses her belief that Coulson was not responsible and that they do not know the whole story, but Jiaying cuts her off and asks them to leave so that she can rest and heal.
Meanwhile, as Hunter and Fitz try to find Bobbi, Fitz demonstrates that he is recovering from his aphasia by finishing Hunter's sentences, much to Hunter's annoyance. Fitz then starts pulling up footage of Bobbi before she left the Playground.
Back at Afterlife, Skye approaches Raina, realizing that Raina had forseen the attack on Afterlife, to which Raina admits. Raina correctly knows that Skye wants to know what will happen next, but Raina notes that Skye would not believe anything she said even if she told her. Raina tells Skye that her destiny is to help Skye become the leader of the Inhumans, explaining that Jiaying is misleading them right now, and promises her that she will see the truth. Skye does not believe this, and Raina tells Skye that the two will never speak to each other again.
Gordon teleports into Jiaying's room with the captured agent and tells Jiaying that he has taken all the Inhumans who needed protection back to their homes, while the others are ready to fight. Jiaying is sure that Lincoln will fight with them as well, and she and Gordon note that all the Inhumans are convinced that S.H.I.E.L.D. is a threat as a result of her plan. When Gordon asks whether Skye will fight with them, Jiaying expresses her certainty that Skye will. Jiaying then proceeds to heal herself by grabbing the agent and draining him of his life force, thus revealing for the first time the source of her longevity.
May, Simmons, and Zabo arrive at the Playground, and Coulson asks Zabo what he is really doing here. Zabo claims to be a "peace offering" and rambles insanely before being taken him to his cell. Simmons shows Coulson the three empty vials found in Cal's pockets that she is about to analyze in the lab, believing that Zabo had taken them before handing himself over. Coulson then anxiously asks May if they have lost Skye, but a bitter May replies that Skye chose to side with the Inhumans.
Having pulled up the footage, Fitz and Hunter see Bobbi leaving the base with May, only to see May leaving the base with other agents 10 minutes later. Hunter realizes that Bobbi had really gone with Agent Kara Palamas, but he and Fitz do not know why she would kidnap Bobbi.
Meanwhile, Bobbi has her hands handcuffed to a table in a room in an abandoned building. Kara and Grant Ward then arrive, and Ward explains to Bobbi that while they were brainwashing him, Sunil Bakshi had told the two that Bobbi had knowingly turned Kara over to HYDRA, resulting in her torture and brainwashing. They now want Bobbi to admit this to them, so that Kara can achieve closure. Having learned from Kara about Bobbi's dislike for them, Ward shows Bobbi that he intends to torture her with needles.
Skye visits Jiaying later and is amazed to see her healed and standing, but Jiaying attributes this to her Inhuman powers, Skye's presence, and her doctor's treatment. Jiaying tells Skye that they need to ensure the Inhumans' safety, but Skye points out that S.H.I.E.L.D. can find them anywhere (not knowing about the tracking device's destruction). Jiaying replies that they have to come out of hiding and fight S.H.I.E.L.D, pointing out that Skye knows especially well how S.H.I.E.L.D. discriminates against those who are different and gifted. Jiaying tells Skye that the only way she knows that they will defeat S.H.I.E.L.D. is if Skye fights alongside her. Jiaying then gives Skye the necklace she had received from Gonzales and tells her to return it to her if she decides to fight with her.
Back at the Playground, having discovered video footage of the inside of the hijacked quinjet, Coulson, May, and Simmons realize that the entire attack was orchestrated by Jiaying so that she could convince Skye and the other Inhumans to join her in fighting S.H.I.E.L.D. Hunter and Fitz arrive to show the trio what happened to Bobbi. Fitz explains that Kara had murdered her guard and hid his body before using her Photostatic Veil to disguise herself as May. Fitz and Hunter were able to track the quinjet to Spain, so Hunter and May decide to head there to find Bobbi. As Hunter, May, and several other agents prepare to go to Spain, Coulson accompanies them and expreses his suspicions to Hunter and May that Ward is involved, although they still have no idea why Kara took Bobbi hostage. May simply announces her intentions to kill Ward when she finds him.
Meanwhile, Ward tells Bobbi that he knows good agents will be able to push away pain while under torture. Therefore, he has injected Bobbi with a paralytic and an anesthetic so that she cannot fight what is happening to her or feel the pain. He then sticks needles underneath her nails. He then explains that the anasthetic will wear off in a little bit, and a huge amount of pain will suddenly flood through her. Ward offers to stop this if Bobbi confesses her "sins." Bobbi acknowledges that what Kara went through was terrible but explains that she had to choose between giving HYDRA the location of a safe house that might have been occupied or blowing her cover and losing intelligence that would save the lives of 24 S.H.I.E.L.D. agents. She claims that the lives of many outweigh the life of one person and that Kara had sworn the same oath when she had joined S.H.I.E.L.D. When Ward expresses his disgust with Bobbi's "apology," Bobbi tells him and Kara that any apologies or pleas for mercy she makes under torture will all be false.
On the Iliad, Weaver and Oliver inform Coulson that Gordon had destroyed the tracking device and because they know longer know the Inhumans' next move, they should attack them now. Coulson refuses to do until he knows more and points out that they may still have assets among the Inhumans. Realizing that Coulson is referring to Skye, Weaver and Oliver express their skepticism for relying on Skye. Mack then arrives and tells Coulson, Weaver, and Oliver that he needs to see the matter with the Inhumans resolved before leaving. However, Mack believes that S.H.I.E.L.D. should not attack. Coulson then acknowledges that Skye might be a threat but that she is the only way that the Inhumans and S.H.I.E.L.D. can reach a peaceful resolution. He asks for some time to get information from Cal, and Weaver gives him three hours to do so. Mack asks Weaver about the alien cargo, suggesting that the Inhumans are fighting because of that, and Weaver explains that she has doubled the amount of security to guard it. Weaver then orders Mack, the ship's former chief engineer, to prepare it for battle.
Coulson arrives at Cal's cell to find him shivering and wrapped in a blanket. Zabo complains about the cold and the bracelet attached on his wrist. Coulson explains that the bracelet is monitoring his vital signs. Coulson demands to know why Jiaying sent him, but Zabo tells him that because Coulson does not have any children, he will never understand what a father will do for his child, citing the pain he felt when S.H.I.E.L.D. kidnapped Skye as a baby. Coulson reminds Zabo that HYDRA was responsible for that, not S.H.I.E.L.D., and points out that Zabo got his revenge by murdering a village of people. When Coulson asks how Zabo did it, Zabo simply replies, "With style."
Coulson goes to Simmons at the lab to find out about the drugs that Zabo took. Simmons explains that Zabo took various drugs with the intention to give himself superhuman strength. When Coulson asks if Zabo will survive, Simmons points out that a single vial of the drugs would kill a normal man and that Zabo took three and should have died already.
Meanwhile, Kara can see in Bobbi's eyes that she is now feeling the pain. Bobbi tries to manipulate Kara into turning against Ward, but Kara reveals that Ward has told her everything about his past, including his abusive family, his recruitment to HYDRA by Agent John Garrett, and his murder of Agent Victoria Hand. Kara explains that she loves Ward and will stand by him no matter what he does because he was able to overcome his family and the pain that Garrett made him undergo to remake himself.
At night, Jiaying meets with Raina and apologizes to Raina for not listening to her earlier warnings. Jiaying then asks Raina if she would use her visions to be an advisor to the Inhumans.