The Closure of the Fear Dimension's Rift was the result of Phil Coulson using a Gravity Containment Device created by Leo Fitz to contain the so-called "Fear Dimension" which had opened in the Lighthouse.
Having been lured into the St. Louis Aerospace Facility by General Hale, S.H.I.E.L.D. brought back the Kree Orb which had been used to trick them into the Lighthouse, stored along with the Monoliths. However, it turned out that the Kree Orb had been rigged with a bomb. Although the Chronicom Noah attempted to contain the explosion, the blast destroyed the three Monoliths, creating a spacetime rift onto what Leo Fitz called a Fear Dimension.
The Fear Dimension generated several illusions out of the S.H.I.E.L.D.'s agents' minds. These illusions attempted to murder them on several occasions, prompting Fitz to create a Gravity Containment Device in order to end the phenomenon and avoid that it spreaded outside the Lighthouse. However, the device needed to be put right into the rift, putting the one accomplishing the mission in real danger. Phil Coulson offered to be the one, which triggered an argument and ultimately forced Coulson to reveal that he was dying.
Equipped with a gas mask, a gun and the Gravity Containment Device designed by Leo Fitz, Phil Coulson went down into the subterranean levels of the Lighthouse. He soon encountered an illusion of Mike Peterson, who told him that the air was breathable. Although Coulson held him at gunpoint, Peterson promised that he would not try to harm him nor would he keep Coulson from fulfilling his mission.
However, Peterson also hinted that not only he was not real, but that everything Coulson believed to have lived since the creation of his team was fake as well and that Coulson was still on the operation table being resurrected. At first, Coulson elected to ignore what Peterson claimed, but Peterson insisted that everything he said was true, explaining that Coulson had lived in his mind what he wished to have lived in real life.
Coulson refused to believe what Peterson said, but his counter-arguments progressively lost in conviction, to the point that Peterson was able to take Coulson by the arm and slowly lead him to the Fear Dimension rift. However, at the last moment, Coulson retook control and told Peterson he did not believe him. Angered, Peterson tried to forcefully take Coulson to the Fear Dimension, only to be destroyed by the real Deathlok, who had been brought to the Lighthouse by Deke Shaw.
As Deathlok helped Coulson to get back onto his feet, they were attacked by another illusion in the form of Lash. Deathlok jumped over it and destroyed it by firing a rocket at it. Then, two illusions of Vrellnexians joined the battle. Deathlok destroyed one while Coulson picked up the Gravity Containment Device he had dropped earlier and shot at the other creature, causing them to vanish.
Coulson ultimately activated the Gravity Containment Device, which automatically levitated towards the rift. Upon fitting into the rift, the Gravitonium embedded in the device released its potential, causing Coulson and Deathlok to be drawn towards the rift. In the same time, they were attacked by a last illusion: Hive.
Coulson and Deathlok managed to resist the attraction of the Fear Dimension and to destroy the illusion of Hive, which vanished like the others. Eventually, the device successfully shut down the Fear Dimension, much to Coulson's and Deathlok's relief.
However, the device did not permanently and completely shut down the Fear Dimension, which kept generating illusions from time to time. Therefore, S.H.I.E.L.D. searched for more Gravitonium to create a more reliable device to contain the Fear Dimension. Although they successfully got some in the Principia, Fitz had trouble compressing the element enough to create a new Containment Device.
It ultimately took a serious psychic split from Fitz, causing the release of his dark personality of The Doctor and the forced and painful removal of Daisy Johnson's Inhuman Control Device to eventually have a way to compress the Gravitonium and create a new Gravity Containment Device. This new device was taken by Johnson to the partly contained Fear Dimension: both the Containment Devices were combined and permanently shut down the Fear Dimension.
Unknown to everyone, when Phil Coulson closed the rift to an alleged Fear Dimension, the Black, White, and Grey Monoliths created a copy of him that was sent through time and space hundreds of years ago and to a world inhabited by non-corporeal beings, where an individual known as Pachakutiq took over his body. When this happened, Coulson's memories intermingled with Pachakutiq's in a fashion that caused both sets of memories to be clouded, causing Pachakutiq to believe that he had had a family that his lover Izel had murdered. This led him to start a crusade to kill her and wipe out the Shrike, adopting the name Sarge. His evil doppelgänger was eventually killed by Alphonso Mackenzie with Izel before they could doom Earth.