All the Comforts of Home is the eleventh episode of the fifth season of the television series Agents of S.H.I.E.L.D., and the ninety-ninth episode overall.
Coulson and the team set out to rewrite the course of humanity's fate; they're unaware that their efforts will dramatically change one S.H.I.E.L.D. agent's life.
General Hale visits her daughter Ruby in her bedroom, and chides her for having skipping classes and her obsession for Quake. While her mother is leaving, Ruby asks her whether she considers herself a good person as she is chasing the S.H.I.E.L.D. agents, who are supposed to be working for a better world. Hale assures her daughter that she is doing everything for Ruby.
The full team of S.H.I.E.L.D. agents returns in their time and discovers that they are still in the Lighthouse, which was designed as a safe bunker for an old S.H.I.E.L.D. project. While Jemma Simmons examines Alphonso Mackenzie's wounds, Melinda May and Leo Fitz try to find some communication equipment. Phil Coulson remains with Daisy Johnson, who regains consciousness and is told by Coulson that he would never give up on her. May and Fitz are shocked to discover three Monoliths in a storage room: one black, one white and one grey. They also encounter Noah, a Chronicom.
Noah explains that the Monoliths' origin is unknown and that he monitors the Earth activities from the Lighthouse. One particular event troubles the team: beams of light seemingly coming from space onto Earth, similar to what Samuel Voss mentioned to Coulson. They decide to leave to investigate the place, with the exception of Johnson, who prefers remaining at the Lighthouse with Noah for everyone's security. The team arrives in the small city of River's End, where they borrow a van to go to the place where Fitz left the Zephyr One.
Aboard the Zephyr One, Fitz and Simmons discovers that the light beams are not what they look like and identify their origin: the Kree Orb used by Hive at Union City. Elsewhere on the plane, Yo-Yo Rodriguez expresses her concern to Mackenzie about what her future counterpart warned her about.
The team infiltrates the St. Louis Aerospace Facility, where they find S.H.I.E.L.D. Agent Piper, who tells them that she is also here to investigate and try to deactivate the Kree Orb. Piper tells her colleagues that she looked for them, but to no avail, while eluding the authorities.
Fitz and Simmons discover that the Kree Orb was rigged with a timer to regularly activate it. As masked and heavily armed figures storm the place, Piper reveals that she actually made a deal with General Hale. However, Piper was convinced that no harm would be done to the S.H.I.E.L.D. agents and that they would simply be taken to Hale. Actually, the masked men intend to kill them all and a brutal fight erupts in the facility, during which the S.H.I.E.L.D. agents discover that they are fighting androids. While several of them are taken down, the attack team's leader, a masked feminine figure, uses chakrams and severes Rodriguez's arms. Despite that, the team manages to retreat and returns to the Zephyr One.
Meanwhile, contrary to what everybody, including himself, believed, Deke Shaw was not killed when the White Monolith was activated. Insetad, he was transported in the present as well. Amazed by everything he sees, Shaw eventually enters in a bar, where he gets drunk and realizes that he has nothing to pay for the drinks. He tries to escape, but he is arrested and taken to River's End Police Station. Johnson discovers Shaw's arrest and decides to have him getting out of custody before he tells anyone about S.H.I.E.L.D., although Noah advises her against it.
Johnson poses as Shaw's social worker and convinces Chief Wellins to let him out. Meanwhile, Officer Kennedy appears to recognise Daisy and appears to have contacted the military. In the meantime, Johnson and Shaw manage to leave the police station and return to the Lighthouse. As it turns out, the military was actually contacted by Agent Piper, prompting Hale to send forces to River's End to find the S.H.I.E.L.D. agents. May contacts Daisy and she perceives that something went wrong during their mission. She boards the Zephyr One with Shaw and learns about what happened to Rodriguez, who is taken to surgery.
The leader of the androids turns out to be Ruby, who returns to her room where her mother confronts her about what happened. Ruby claims that since Johnson was not there, she hurt her friends to have her showing herself. Hale leaves the room, which happens to be a guarded room in a secret base, stating that the Kree Orb the S.H.I.E.L.D. agents took will do its job. Indeed, as Fitz, Johnson and Noah study the artifact, it suddenly heats up. Noah figures out that it will explode and sends Johnson and Fitz away before attempting to limit the range of the explosion which destroys him.
General Hale finds Carl Creel and informs him that she is putting together a team she wants him to be in.