Season 1

Complete listed story — includes the ending

1. Pilot

Following the Battle of New York, Agent Phil Coulson, having survived his apparent death before the battle, assembles a team of agents ( Melinda May, Grant Ward, Leo Fitz, and Jemma Simmons ) to investigate superhumans and other related phenomena, which are now public knowledge. Their first assignment involves Mike Peterson, who was supplied with an Extremis -containing serum by Project Centipede. Skye, a member of the hactivist group the Rising Tide who saw Peterson in action, warns him about S.H.I.E.L.D. and offers to help him, but he declines. While visiting the scene where Peterson rescued a woman from a burning building, the team learns that the fire was caused by another subject exploding because of Extremis. Skye is kidnapped by Peterson, who is now on the run, and makes her erase all his personal information. Coulson's team is able to track them down and subdue Peterson, taking him into S.H.I.E.L.D. custody. Viewing Skye as an asset, Coulson offers her a place on his team.

2. 0-8-4

Skye is now integrated into Coulson's team as a consultant. Their next assignment is in Peru, tracking an "0-8-4", the S.H.I.E.L.D. code for "an object of unknown origin". Once there, the team quickly realizes that the object is a piece of forgotten Hydra technology powered by Tesseract energy. Coulson meets with a former colleague and officer in the Peruvian military, Camilla Reyes, and brings her team aboard their plane, the Bus. Reyes betrays Coulson in order to take the Hydra weapon for her government so they can defeat Peruvian rebels. The squabbling team members band together and take out Reyes' men. When the plane lands at a S.H.I.E.L.D. base, Reyes is taken into custody. Later, Skye is revealed to still be loyal to the Rising Tide, while Director Nick Fury scolds Coulson for the damage to the plane and warns him of the risk Skye poses.

3. The Asset

S.H.I.E.L.D. searches for one of its assets, Dr. Franklin Hall, who was kidnapped by Ian Quinn, CEO of Quinn Worldwide, using a gravity-based device. Quinn wants to use Hall to take control of the planet's gravity by building a giant " gravitonium " generator. Heading to Malta with the team, Skye volunteers to infiltrate Quinn's mansion during a party so that Coulson and Ward can rescue Hall. Skye tricks Quinn into believing she is betraying S.H.I.E.L.D. for the Rising Tide. However, Coulson soon discovers that Hall perpetrated his own escape in order to find and destroy both the gravitonium and the generator. Coulson warns him that doing so would end up killing millions. Their violent disagreement forces Coulson to send Hall into the generator, seemingly consuming him, but shutting the machine down at the same time. Coulson orders that the gravitonium be placed under high security off the books at S.H.I.E.L.D.; however, no one notices that Hall is still somehow alive within the gravitonium.

4. Eye Spy

Coulson and his team investigate a series of diamond thefts by Coulson's former protégé Akela Amador, who is being blackmailed by an unknown handler using an explosive cybernetic eye. Coulson is able to take Amador to the Bus, while Fitz and Simmons create a pair of glasses that hijack her feed. This allows Ward to carry out Amador's mission while the team attempts to disarm and remove her cybernetic eye. Ward completes the mission, discovering mysterious carvings, while Coulson finds who he thinks is Amador's handler, only for that man to be killed through a similar device to Amador's. With the cybernetic eye now removed, Amador is taken away by S.H.I.E.L.D. agents, though Coulson promises her she will have a fair trial in which he will testify for her. Before she goes, Amador tells May that something seems different to her about Coulson.

5. Girl in the Flower Dress

The team attempts to find Chan Ho Yin, a Chinese street performer with pyrokinetic abilities, after he is kidnapped by Project Centipede recruiter Raina. Raina injects him with Extremis to increase his power, before harvesting his blood platelets for further experimentation. Skye knows a hacker who could have released the information on Chan's location and abilities; she secretly sleeps with him, trying to discover the truth. May finds them and, not trusting Skye, arrests them. S.H.I.E.L.D. attacks the Centipede facility and attempts to help Chan, but he refuses and May activates the unstable Extremis within him to kill him. Coulson questions Skye and she reveals that she joined the Rising Tide and S.H.I.E.L.D to find her parents. Coulson agrees to help her, but fits her with a device to block any computer access. Raina visits Centipede member Po in prison, telling him to inform the " Clairvoyant " of the experiment's results.

6. FZZT

The team investigates a series of deaths involving levitation and electrostatic anomalies. Although the team initially assumed the deaths were caused by some form of weapon, the cause is found to be an alien virus from a Chitauri helmet salvaged from the Battle of New York. When Simmons is infected by the fatal virus, she and Fitz work feverishly on a cure while Coulson ignores a direct order from Agent Felix Blake to sacrifice Simmons and save the rest of the team. With time running out and unaware that their last attempt at a vaccine was successful, Simmons leaps from the plane, though Ward manages to save her by jumping out after her and inoculating her before she dies. May tells Coulson, who feels differently than he did before he died, that anyone would be changed by such an experience. The helmet is delivered to Agent Blake, who warns Coulson of the consequences of disobeying a direct order from headquarters, though Coulson dismisses this, accepting that he is different now.

7. The Hub

At The Hub, a S.H.I.E.L.D. command facility, Agent Victoria Hand assigns Ward and Fitz to a mission in South Ossetia, where they must disable a weapon called "the Overkill Device", which turns enemy weapons against their users. Skye and Simmons try to find more information about the mission, which has been classified as Level 8, with Simmons tranquilizing Agent Jasper Sitwell when he catches her hacking into Level 8 files. Skye learns that there is no extraction team for them and informs Coulson, who takes his team to rescue Ward and Fitz, who are successful in their mission. Later at The Hub, Coulson discovers that the person who brought Skye to the orphanage was an unidentified S.H.I.E.L.D. agent. However, Coulson does not tell Skye the entire truth about the file and asks May to discreetly investigate further. Coulson is later denied access to information about his recuperation in Tahiti, despite his Level 8 clearance.

8. The Well

The team looks into a plot to find and assemble three parts of an Asgardian Berserker Staff which imbues the holder with super strength and an uncontrollable rage. They are opposed by a pagan hate group that has already discovered the first piece of the staff. With Thor off the grid, Coulson's team is assisted by Dr. Elliot Randolph. While retrieving the second piece of the staff, Ward touches it and relives a traumatic childhood memory involving his abusive older brother. He becomes irritable, aggressive, and much stronger. After the team realizes that Randolph is an Asgardian who has lived on Earth for centuries, he gives them the location of the third staff piece. Once the team recovers it, Ward and May use the completed staff to defeat the pagans. In a hotel, Ward declines Skye's invitation to talk, instead following May into her room, while Coulson has a nightmare about his recuperation in Tahiti.

9. Repairs

A mysterious force threatens Coulson's team when they bring in a safety inspector named Hannah Hutchins, who is blamed for an explosion that killed four technicians and who Coulson believes has subsequently developed telekinesis. After the plane makes an emergency landing, the team discovers that the mysterious force is one of the technicians named Tobias Ford who is trapped between Earth and " Hell " following the accident. Ford "targets" Hutchins to protect her from those who would try to harm her. It is later revealed that Ford caused minor safety issues and filed safety reports to spend time with Hutchins. One of his issues inadvertently caused the explosion. May manages to defeat Ford and convinces him to let go, causing Ford to disappear to an unknown location. Coulson tells more about May's difficult past and how he wants to help her recover. May later pulls a prank on Fitz, revealing that she is healing.

10. The Bridge

Coulson recruits Peterson to his team for super soldier support when Edison Po is sprung from prison by upgraded Centipede super soldiers. Coulson's team traces a Centipede-powered soldier to an abandoned factory and is ambushed by a squad of super soldiers who were subjected to the same eye implant as Akela Amador. Po recommends Raina stop inquiring after the Clairvoyant, as it could mean her death. Meanwhile, Coulson and May are keeping information regarding Skye's parents from her. When Peterson contacts his son, Ace, he learns that he has been kidnapped by Centipede, who suggest a trade – Peterson for his son. Coulson escorts Peterson to the arranged exchange, where Peterson reveals that Centipede wants Coulson, not Peterson. Coulson agrees to be taken prisoner. After the exchange, Peterson attempts to rescue Coulson, but is apparently killed in an explosion. Raina tells Coulson that they want to know how he was resurrected.

11. The Magical Place

Victoria Hand leads S.H.I.E.L.D.'s efforts to rescue Coulson while Centipede tortures him to learn the secret of his resurrection. Believing Skye to be untrustworthy and after seeking May's input, Hand has Skye removed from the Bus. Skye sets out on her own investigation, which leads the team to Coulson's location. After the Clairvoyant kills Po, Raina takes over Coulson's interrogation. She uses a scanning device to compel him to remember aspects of his being brought back to life. As Coulson experiences flashbacks, the team rescues him after capturing Raina. Coulson confronts Streiten, who tells Coulson he had been dead for days and was resurrected on the orders of Director Fury. Streiten reveals that, after his revival, Coulson had lost the will to live and the doctors manipulated Coulson's brain to give him false memories in order for him to continue his work. It is later shown that Peterson is alive, albeit badly burned, missing the lower half of his right leg and with an explosive surveillance eye implanted in him by someone working for the Clairvoyant.

12. Seeds

While at a S.H.I.E.L.D. Academy, Ward, Fitz, Simmons, and Skye investigate an attack upon Seth Dormer, a popular cadet, with an "ice machine" that can freeze people and their surroundings. Another ice machine soon freezes cadet Donnie Gill, though the agents are able to save him. While the rest of the team interrogates the other cadets, Fitz befriends Gill, seeing much of himself in him, and helps him solve a problem with a new power source. Meanwhile, Coulson and May go to Mexico City to find a former agent named Richard Lumley, who tells them of a mission 21 years earlier involving Skye, an 0-8-4 with apparent superhuman abilities. The team deduces that the cadets are building a bigger ice machine for Quinn and, with the better power source, Dormer and Gill give Quinn a demonstration, creating a massive ice storm. Though the team apprehends Gill, Dormer is killed by the storm and Gill gains apparent cryokinetic abilities. Later, Coulson calls Quinn, who has connections to the Clairvoyant.

13. T.R.A.C.K.S.

Hunting the Clairvoyant, the team boards a train in Italy on which a Cybertek Inc. security group is shipping a package to Quinn. The group is exposed, forcing Coulson and Ward to flee the train. Meeting up with May, they get back to the train and Simmons, but Fitz and Skye are gone, having already followed the package to Quinn's mansion. Skye is confronted by Quinn and discovers the alive Peterson in a hyperbaric chamber. Inside the package is a high-tech prosthetic leg from Cybertek's "Project Deathlok" that Quinn fits onto Peterson's amputated right leg. Peterson goes on to murder the Cybertek guards on the orders of the Clairvoyant, who has once again kidnapped Ace. Quinn shoots Skye twice in the stomach and leaves her for dead. S.H.I.E.L.D. raids the mansion and finds Skye after capturing Quinn. Simmons can only sustain Skye temporarily by placing her in the hyperbaric chamber.

14. T.A.H.I.T.I.

Skye is rushed to a S.H.I.E.L.D. medical facility, but the doctors are only able to stabilize her. Agents John Garrett and Antoine Triplett arrive to take Quinn for questioning, but Coulson refuses to turn him over. Garrett decides to interrogate Quinn on the Bus, learning that the Clairvoyant ordered Quinn to shoot Skye so they could learn about Coulson's resurrection. Fitz and Simmons, after looking over Coulson's files, realize that Coulson was revived at a place known as the " Guest House ", where Coulson, Ward, Garrett, and Fitz head for answers. Fitz finds the needed drug while Coulson discovers a room marked "T.A.H.I.T.I." and the source of the drug, the upper half of a blue-skinned humanoid corpse. Everyone escapes the facility, as it was rigged to explode, and, despite Coulson attempting to stop it based on what he saw in the T.A.H.I.T.I. room, Fitz gets the drug to Simmons in time to successfully save Skye.

15. Yes Men

The Asgardian Lorelei enslaves a biker gang and begins to form an army. The team is summoned to investigate an energy reading from the Bifrost, encountering Sif, who is seeking Lorelei. She explains that Lorelei escaped imprisonment during the attack of the Dark Elves and, to neutralize her power of controlling the minds of men, Sif must fit a special collar around her neck that prevents her from speaking. They fight Lorelei and her men, but Lorelei enchants Ward and they commandeer the Bus. Lorelei tells May that Ward loves someone else. While May fights Ward, Sif confronts Lorelei and fixes the collar to her neck, undoing her enchantment. Sif returns Lorelei to Asgard and May ends her relationship with Ward. Coulson tells Skye the origin of the drug used to revive them but, despite how disturbed Coulson is by this fact, Skye remains optimistic. He orders Skye to keep the origin of the drug a secret until Fury gives them the truth. Unknown to them, May is monitoring their conversation and reporting to someone else.

16. End of the Beginning

Agents Garrett, Triplett, Hand, Sitwell, and Blake join the team in hunting the Clairvoyant. The agents pair up to pursue different candidates. While searching for Thomas Nash, May and Blake encounter Peterson/Deathlok and tag him with a tracker. They soon converge on his new location while Triplett and Simmons stay at the Hub with Hand. The team finds Nash, a vegetative man on life support who communicates through a computer. When Nash boasts about being the Clairvoyant and says that Centipede will kill Skye, Ward kills him. Coulson and Skye soon realize that Nash was not the Clairvoyant, but that the Clairvoyant is a high-ranking member of S.H.I.E.L.D. Coulson accuses Ward of working with the Clairvoyant and shooting Nash, but they are interrupted when Fitz discovers May's secret phone line. As Coulson and Skye standoff with May in the hangar, control of the Bus is hijacked by the Hub, where Hand orders everyone onboard to be killed.

17. Turn, Turn, Turn

After the Bus is hijacked, Garrett's jet is attacked by S.H.I.E.L.D. drones and he rejoins the team. At the Hub, Simmons and Triplett begin working together to secretly upload her research on Skye's blood, only for a Hydra assault on all S.H.I.E.L.D. facilities to force them into hiding. Coulson locks May in the interrogation room with Ward, still believing she is the traitor. Skye discovers a secret code in a signal on S.H.I.E.L.D.'s network that she deciphers to reveal Hydra's infiltration. When the Bus arrives at the Hub, the group splits into teams to capture Hand. However, Hand reveals that she is not a member of Hydra, but believes that Coulson is, recruiting Triplett and Simmons to aid her in stopping them. Garrett accidentally discloses information that reveals himself as the true Clairvoyant and is captured by Coulson and May. Ward accompanies Hand to the Fridge so he can see to Garrett's imprisonment personally, but shortly reveals his own allegiance to Hydra by killing Hand and freeing Garrett.

18. Providence

Ward frees Raina and introduces Garrett to her as the Clairvoyant. Though disappointed that he is not actually clairvoyant, she agrees to try to replicate the "Guest House" drug. Colonel Glenn Talbot sends a military team to the Hub, so Coulson leaves with the team and Triplett, ordering Skye to erase all their identities, including Ward's. Coulson discovers a message with coordinates in the Canadian wilderness where they find the hidden S.H.I.E.L.D. base Providence run by Agent Eric Koenig. Coulson learns from Koenig that Fury is alive, but is told to keep the information secret. He also learns from May that Fury did not oversee the T.A.H.I.T.I. project. Ward and Garrett infiltrate the Fridge, freeing its prisoners and stealing weapons, including the Berserker Staff, the 0-8-4 from Peru, and the gravitonium. Raina informs Garrett that the hard drive containing all of Simmons and Skye's research is locked and only Skye can access it, prompting Garrett to send Ward to Providence.

19. The Only Light in the Darkness

Koenig subjects Coulson's team to a rigorous lie detector test, which Ward narrowly beats to maintain his cover. Coulson takes Fitz, Simmons, and Triplett to stop Marcus Daniels, a superhuman and former Fridge inmate possessing the Darkforce who is obsessed with cellist Audrey Nathan, Coulson's former love interest. After rescuing Nathan, they devise a plan to lure out Daniels. The group overloads him with energy, causing him to explode. Coulson covertly comforts Nathan before withdrawing, as he plans on telling her he is alive some other day. Meanwhile, May leaves the team, tired of Coulson not trusting her. Skye and Koenig hack the NSA to get eyes on the Hydra attack at the Fridge, forcing Ward to murder Koenig to prevent discovery. Skye finds Koenig's body and realizes that Ward is with Hydra. In order to avoid suspicion by Ward, Skye joins him as they steal the Bus before Coulson and the others return to Providence. Later in Ontario, Canada, May is picked up by her mother, who helps her look for Maria Hill.

20. Nothing Personal

Fitz finds a message left by Skye informing them that Ward is a member of Hydra. Hill and a Special Forces team led by Talbot arrive at Providence, where Hill tries to convince Coulson's team to surrender themselves. However, upon hearing of Ward's betrayal, Hill decides to aid the team directly in their hunt. Skye leads Ward to the diner where she met Peterson and secretly tips off the police. She reveals that she knows his secret and escapes while he fights the police, but she is captured by Deathlok. As Ward tries to fly the Bus away, he is confronted by Hill and Triplett, who stall long enough for Coulson to sneak on board. Coulson frees Skye and they escape. The team retreats to a hotel, where Skye reveals she left a trap in the hard drive. Hill departs for D.C. while May returns and shows Coulson the contents of a flash drive she recovered from his false grave. The file is a video of Coulson himself, who was apparently the head of Project T.A.H.I.T.I., informing Fury that the project must be shut down due to its horrific side effects.

21. Ragtag

In flashbacks, a teenage Ward is seen in juvenile detention where he first meets Garrett and accepts his offer to join his organization. Over the years, Garrett trains Ward and eventually tells him about Hydra. In the present, Coulson and May infiltrate Cybertek (who they realize is connected to both Centipede and Hydra) and learn that Garrett was the first Deathlok, his implants are failing, and he needs the Guest House drug to survive. The team travels to Havana, Cuba, discovering the recently abandoned Hydra base, and Fitz and Simmons find the captured Bus. The latter are caught by Ward and taken aboard the Bus, which departs. Fitz disables Garrett's implants with an EMP and the dying Garrett orders Ward to kill them. After the two agents lock themselves in the Bus ' infirmary, Ward ejects it into the ocean. Raina injects Garrett with her synthesized Guest House drug. Initially, it seems to cause an Extremis reaction, but Garrett recovers. Quinn attempts to sell Deathlok soldiers to the military and invites them to tour Cybertek's facility.

22. Beginning of the End

At Cybertek, Quinn begins his presentation to U.S. military officials, only for Garrett to interrupt and kill one of them. Evading the Centipede soldiers, Coulson and his team attack the Cybertek facility, with Quinn and Raina escaping with the gravitonium, Skye saving Ace, May defeating Ward, and Coulson confronting Garrett. Fury rescues Fitz and Simmons, though Fitz is barely alive, before joining with Coulson to face Garrett, who is ultimately dispatched by Peterson when he learns that Skye has saved Ace. Peterson, unable to face his son, goes off on his own to redeem himself. Fury expresses his respect for Coulson, who he sees as an Avenger, and appoints him the new Director of S.H.I.E.L.D., leading the team to a secret base run by Agent Koenig's brother, Billy. Raina delivers a photo of Skye to a mysterious man, telling him she has found his daughter. Later, Coulson awakens in the middle of the night and begins exhibiting signs of the same enhanced mental capacities and fixation that Garrett experienced, compulsively carving strange symbols into a wall.