The Winter Soldier had returned to the Earth after being alerted of a catastrophic event. The trail he followed led him to a S.H.I.E.L.D. facility. After infiltrating the building, he managed to play back an holographic recording of the events that happened in a laboratory; a group of scientist died as a consequence of an explosion in the middle of some experiment, with the only survivor being a small eerie girl. Bucky was soon caught off-guard and attacked by S.H.I.E.L.D. agents.
In the middle of the woods, a young blond man woke up suffering from amnesia. After being brought to the nearby town of Pleasant Hill, he was examined by doctors. The young boy overheard them suspiciously talking about a program, prompting the boy to run away. After being knocked down by S.H.I.E.L.D. agents, the amnesiac boy woke up again, and was convinced to try to accomodate to the town. He tried to escape again, finding a force field in the limits of the city before being knocked down. Nineteen days went by, and the boy, who had taken the name of "Jim," had become a member of the community, no longer trying to escape.
One day while walking on the park, Jim encountered the eerie girl, who was taken away by an adult after seemingly bringing a bird back to life. Thirty-six days into Pleasant Hill, Jim attended to a house fire. The arsonist confronted Jim inside the house, revealed to him that his life in Pleasant Hill had been a lie, and requested a meet up in case Jim wanted to uncover the truth.
On day forty, Jim met up with the mysterious man, a mechanic named Phil who had subconsciously created a device that allowed people to return to their normal selves. "Phil" had also stolen a training video in which S.H.I.E.L.D. Director Maria Hill gave a tour around Pleasant Hill, describing it as the future of super villain incarceration, where its prisoners were turned into mild mannered individuals using reality-warping technology derived from the Cosmic Cube called "Kobik." In the video, it was shown how the super villain Graviton was turned into innocent Pleasant Hill inhabitant Howie Howardson. After using Phil's device on themselves, the true forms of Jim and Phil were revealed, those of Baron Zemo and the Fixer, now swearing to use the device to free more prisoners and turn Pleasant Hill into dust.
In the S.H.I.E.L.D. Helicarrier, Commander Steve Rogers followed the trail of the Winter Soldier, after he had assaulted the flying headquarters of the organization, as part of several other attacks. He was left a message in the form of a napkin of a diner they used to frequent. Meanwhile, Captain America was urgently contacted by the Whisperer after defeating the Green Skull.
As Steve met Bucky at Bev's Diner and Sam met the Whisperer, revealed to be Rick Jones, at his New York home, both heroes were informed by Bucky and the Whisperer, respectively, of S.H.I.E.L.D. having never discarded the Kobik program as it was believed when its existence had been made public by the Whisperer. Both had a lead, of a town in Connecticut. Bucky left Steve as he was being picked up by S.H.I.E.L.D. agents, and Sam left with Rick Jones after his home had been surrounded by S.H.I.E.L.D. forces.
Now having learned about Kobik's continuing existence, Steve Rogers confronted Maria Hill, who brought him to Pleasant Hill. Maria Hill presented the town to Steve, and revealed its secret, that most of its inhabitants were reformed super villains. When Rogers demanded to know where were the fragments of Cosmic Cubes used for Kobik, she directed him to the eerie little girl, who was the fragments of the Cosmic Cube having taken the form of a near-omnipotent child.
In secret, several of Pleasant Hill's inhabitants had already had their memories returned by the Fixer, including Moonstone and the Trapster. The villains, led by Zemo, soon unleashed a co-ordinated assault, revealing their true forms and attacking the S.H.I.E.L.D. outpost that served as the town hall.
Captain America and the Winter Soldier arrived to Pleasant Hill, which had descended into chaos. Together they rescued Agent Kincaid from the Blood Brothers, unaware that she wanted to be taken hostage so she could infiltrate the town hall, which had been turned by Zemo into a lock-up to hold numerous staff members and citizens hostage. The two heroes offered to help her in a plan to retrieve a powerful item from the Pleasant Hill Museum to use against the villains, disabling the security from a remote station so she could access it.
After convincing Zemo to let him get medical help for the severely injured Maria Hill, Steve Rogers was scorted by Father Patrick to the clinic of Erik Selvig, Kobik's caretaker. Unbeknown to anybody at all, Father Patrick was actually the Red Skull in disguise, and the person responsible for having ignited the situation at Pleasant Hill.
With the objective of finding Kobik in mind, Rogers was given by Selvig the suggestion of looking for Kobik in her favorite location, the bowling alley. Unfortunately, after getting hold of the small girl, Steve was brually attacked by Crossbones. On the brink of Steve's death, Kobik used her power to restore him to his prime, granting him the power necessary to gain the upper hand against Crossbones. After defeating Crossbones, Steve was joined by Captain America and the Winter Soldier.
With Kobik having disappeared after restoring Steve, the three heroes set out to find her again, but they were not alone in the search for her. Baron Zemo had the Fixer create a device capable of containing Kobik and stripping her of her sentience, planning to defeat the Avengers with its power. Under the orders of Zemo, Kraven the Hunter led a group of villains to find her. With the search for Kobik bearing no results, Steve decided to change the plan and take the fight directly to Zemo before he could find her, rallying all of the heroes in the town.
Meanwhile, Kraven the Hunter managed to successfully lure Kobik into a device created by the Fixer to contain her. While they were bringing her to the town hall, Agent Kincaid had managed to get to the museum, where its curator revealed himself to be the retired hero Wendell Vaughn, a.k.a. Quasar, and gave her the items of power she was looking for, his former Quantum Bands.
Back in the town hall, Zemo was about negotiate with the Avengers the safety of the hostages when Quicksilver, Vision and Doctor Voodoo sneakily rescued them. With the civilians and S.H.I.E.L.D. staff safe, both teams of Avengers proceeded to confront Zemo directly. His army of villains held the line to buy the Fixer's device enough time to turn Kobik into a proper Cosmic Cube. Using Graviton's powers, Zemo created a virtually impenetrable shield, and the heroes began to run out of time to stop Fixer's device.
Agent Kincaid stepped in, empowered by the Quantum Bands, and used their power to destroy the shield, disrupting Fixer's device in the process, and freeing Kobik. Both Baron Zemo and Erik Selvig tried to convince Kobik to join their respective sides, but the small child showed her dissatisfaction with the events transpiring in the town due to Zemo's actions, and her disillusion with her experience among humans due to the way S.H.I.E.L.D. used her. She blasted away the Winter Soldier, who had tried to put her down for considering her too dangerous, and teleported both Baron Zemo and Erik Selvig away to the Himalayas before disappearing herself.
With their leader gone, the villains tried to escape from the town. S.H.I.E.L.D. agent Mach VII had managed to send a distress signal, so when the bad guys ran for the hills, they found an aerial barricade waiting for them. With the airborne support blocking the villains, the Avengers proceeded to finish them off.
After the dust settled, Maria Hill was scolded by her superiors in the World Security Council, with her position as director of S.H.I.E.L.D. pending a review; Zemo forced Selvig to come with him, intending to use him on his plans; the leaders of the Avengers teams agreed to keep the situation under the wraps for the time being; Rick Jones was tracked down by Steve Rogers and offered a job at S.H.I.E.L.D. to make amends for his crimes; Agent Kincaid began being trained by Wendell Vaughn to become the new Quasar; Kobik appeared before the Winter Soldier and set out to prove him that she could do good. Before they headed off, Kobik got Winter Soldier's approval to take the "friends" she made at Pleasant Hill with the ; and the Red Skull began to recruit new members into his reborn Hydra.
Agents of S.H.I.E.L.D / New Avengers
After learning of Pleasant Hill and Rick Jones' involvement, a group of S.H.I.E.L.D. agents led by Phil Coulson joined the hunt for him. Deathlok, Quake and Jemma Simmons investigated his house and discovered in a hidden USB his escape route. They followed him to the Morlock Tunnels and apprehended him. During an interrogation at a S.H.I.E.L.D. Battlecarrier, A.I.M.'s New Avengers appeared on scene to retrieve Jones.
A.I.M. had been contacted by Jones through a pre-recorded video that was to be sent to them if the alien nanobots he had ingested noticed him being unconscious. The New Avengers confronted the agents of S.H.I.E.L.D., defeated them in combat, and retrieved Jones. In retaliation for A.I.M.'s involvement, which was considered an act of war, the Pentagon decided to unleash a monster named the American Kaiju on them.
In Avengers Island, the US Army and S.H.I.E.L.D. coordinated an attack on Avengers Idea Mechanics. American Kaiju began to attack the island, forcing Sunspot to deploy their biggest weapon, the Avenger Five. However, while the Avenger Five battled the American Kaiju, S.H.I.E.L.D. launched a major raid on the facilities to retrieve the Whisperer.
A.I.M. finished evacuating the island while the Avenger Five used the exceeding energy from its Gamma reactor to short out the American Kaiju's Gamma enhancements, turning him back to his human form. In the middle of the evacuation, Songbird revealed herself to be a deep-undercover S.H.I.E.L.D agent, and attacked her fellow New Avenger Hawkeye (who had also recently abandoned S.H.I.E.L.D. to help A.I.M.) in the process. When Hawkeye and Rick Jones were about to enter a portal to escape to Avenger Base Two, an A.I.M. agent gave Jones a bad impression of the work they got done there, which, combined with Jones' previous skepticism to ally himself with A.I.M. because of the organization's past, pushed him to abandon them.
Hawkeye was scolded by his superior, Dum-Dum Dugan, for having helped A.I.M. against his fellow S.H.I.E.L.D. agents, while S.H.I.E.L.D. continued searching the island for Jones.
Uncanny Avengers / All-New, All-Different Avengers
In the outskirts of Connecticut, the Avengers Unity Division heeded Steve Roger's emergency call, and while entering the state, they discovered the Wrecker trying to escape in a SUV along with Maria Hill. The Avengers helped Wrecker and Maria Hill evade S.H.I.E.L.D. forces.
In New York City, the recently reassembled Avengers had just defeated an escapee from Pleasant Hill when none other than Maria Hill appeared on the scene on behalf of S.H.I.E.L.D. to keep them out of the current events. However, they received an emergency call from Captain America and were informed about Pleasant Hill. With the Avengers aware of the situation, Maria Hill reluctantly agreed to fly with them to Connecticut. When they were about to land on Pleasant Hill, the Avengers noticed the Unity Division being accompanied by the other Maria Hill. The Avengers' Maria Hill opened fire on them, leading to a brief scuffle between the two teams before they were trapped by Kobik and turned into inhabitants of the small town.
The Avengers and the Avengers Unity Division eventually broke from Kobik's influence due to psychic safeguards in Rogue's mind that she had acquired from her training with Professor X several years ago. After snapping out of the illusion Kobik made her believe, Anna Marie began to recruit the members of both Avengers teams. However, after Vision, the final hero, was recruited, Kobik caught up with the Avengers' actions and confronted them.
Quicksilver rescued the Avengers from Kobik's grasp by spreading them in small groups throughout the city at super speed. It was also revealed that the duplicate Maria Hills encountered by the Avengers were actually prisoners Mindblast and Bloodlust, who had been turned into Maria Hill duplicates to attempt to keep the Avengers out of the conflict. While the Maria Hill encountered by the main Avengers team was acting accordingly, the one encountered by the Unity Squad had tried to use her appearance as a means to escape. The villains soon noticed the presence of the mostly depowered Avengers teams and attacked them mercilessly, heavily injuring and even killing some of them. Deadpool managed to reach out to Kobik and get her to empathize with him based on their shared past of being manipulated beyond their control. Kobik proceeded to do right by the heroes, reviving and healing them, returning them to their prime just in time to heed Steve Roger's call to arms.
Howling Commandos of S.H.I.E.L.D.
In the middle of the chaos, the super villains wreaked havoc across the small town endangering lives. The Howling Commandos of S.H.I.E.L.D. helped contain the chaos during an operation to retrieve their missing member Orrgo, who had been imprisoned in Pleasant Hill and lived a life as a familiy dog before turning back to his normal self. The Commandos also engaged Kobik in combat, but she proved to be too powerful, and teleported them back to their HQs in New Jersey.
One of the numerous immates of Pleasant Hill was the Absorbing Man, who had been turned into an ice cream vendor named Harold. While in Pleasant Hill, Creel fell in love with another immate, Elektra Natchios, who had been turned into the Sheriff Eva.
When Zemo assaulted the small town and the prisoners regained their memories and powers, Absorbing Man began to wreak havoc together with fellow immate Whirlwind. He was convinced by Elektra to spare innocent lives, and Titania and her partner Hood soon appeared to retrieve him, after having learned of his whereabouts.
Creel was deeply affected by his experience in Pleasant Hill, mainly emerging with the desire to live a normal life, noting that he had never been as happy as he was when being Harold. However, he decided to assemble any and every one of the former immates from Pleasant Hill and get revenge on S.H.I.E.L.D. for manipulating their lives.