In the aftermath of The Avengers' battle in New York City, the world attempts to come to grips with the presence of superheroes, gods, and aliens in their midst. Agent Coulson is resurrected under mysterious circumstances and forms an elite team of agents from S.H.I.E.L.D. to keep track of a secret organization known as The Rising Tide. Meanwhile, they must deal with other menaces, such as a man who suddenly finds himself with vast uncontrollable power.
The team heads to Peru to collect an 0-8-4: an unidentified object of great power. Coulson and his people get it, but run across a local commandante, Camilla Reyes... who has a history with Coulson.
Coulson and his team track abducted scientist Franklin Hall to the private manor of a rich industrialist, Ian Quinn. To get in, Coulson has no choice but to send Skye in to lower the laser grid security system so they can stage a rescue.
Coulson and his team try to track down a mysterious woman who has single-handedly committed numerous high-stakes heists. But when the woman's identity is revealed, a troubling secret stands to ruin Coulson.
An elusive girl in a flower dress may hold the key to the mystery that brings Coulson and his team to Asia to rescue a young man with an unusual and dangerous power; and Skye has a secret that jeopardizes her relationship with the team right when they need her most.
A mysterious death by electrocution results in a levitating inactive person. Coulson's team finds another victim and discovers that an alien plague is responsible... and Gemma is the next victim.
S.H.I.E.L.D. sends Fitz and Grant on what turns out to be a suicide mission, leaving Coulson to make a tough decision. Meanwhile, Skye goes looking for information on her parents.
The team investigates an assault in Norway and discovers that a paganist hate group has obtained an Asgardian staff that grants rage and superhuman strength to anyone who touches it. Complications ensue when Grant ends up touching the staff.
The team is called in to investigate a woman who may be generating poltergeist-like phenomena, but soon discover that something much more sinister is involved.
To take on the threat of Centipede, Coulson brings in Mike Peterson, a former test subject who is trying to make a new life for himself as a superhero. However, he soon finds his loyalties tested when Centipede abducts his son in an attempt to get the key to Stage 3.
S.H.I.E.L.D. mobilizes to recover Coulson, who has been abducted by Centipede. Skye is forced to go rogue to find her friend, while Grant and Melinda skirt authority to get results. Meanwhile, Centipede representative Raina offers Coulson the chance to cooperate and learn the secret behind his mysterious resurrection.
The team is called in to investigate a mysterious freezing incident at S.H.I.E.L.D'.s Science & Technology Academy. However, Coulson and Melinda go on a side mission to find the partner of the agent who died delivering a baby Skye to an orphanage, and learn the true story of their teammate's background.
Coulson and his team try to get a lead on Ian Quinn in the hopes he will take them to the Clairvoyant. However, a mission on a train goes awry leaving the team scattered and disorganized... and one of them on the verge of death.
Coulson goes on the attack to save Skye - enlisting the aid of Ward's former S.O. John Garrett and uncovers shocking truths about his own life and S.H.I.E.L.D.
The Asgardian warrior Sif comes to Earth to bring back Lorelei, an enchantress who can seduce men with the power of her voice... and chooses Ward as her new protector.
Coulson organizes three pairs of field agents to hunt down three likely candidates for the Clairvoyant. One of them turns up the Clairvoyant at a terrible cost, but Coulson realizes that not all is at it seems.
A mysterious encrypted signal goes out and S.H.I.E.L.D. is thrown into chaos. Meanwhile, Coulson tries to determine who Melinda is really working for and who he can trust.
In the aftermath of HYDRA's infiltration, S.H.I.E.L.D. is declared a potential terrorist organization. Coulson and his team receive a mysterious set of coordinates and travel to Canada seeking refuge. Meanwhile, the Clairvoyant takes advantage of the chaos to break into the Fridge, release dozens of super-powered criminals, and acquire mystical and high-tech weaponry.
Coulson confirms that one of the escaped prisoners from the Fridge is heading to Portland to continue stalking a woman... a woman that Coulson was once involved with. Meanwhile, Skye and Koenig come up with a plan to learn who was that the Fridge during the breakout.
Coulson and what's left of his team discover what happened at Providence base in their absence. Meanwhile, Skye tries to stall for time so that HYDRA can't get the information on the hard drive. And Melinda finds out the truth about the TAHITI project.
Coulson and Melinda infiltrate Cybertek and learn the origins of the Deathlok project. As the team track HYDRA to their base in Havana, Grant remembers his past and is forced to make some tough decisions about his present.
Dark secrets are revealed as Coulson and his team put everything on the line to stop Garrett and the forces of Hydra. But when the dust settles, Coulson will find that no one's leaving this battle unscathed. And just when all hope seems lost, they're joined by the one man who may be able to turn the tide-Nick Fury.