Missing Pieces is the first episode of the sixth season of the television series Agents of S.H.I.E.L.D..
Scattered across the galaxy, the team works to find their footing in the wake of losing Coulson.
Shortly after the Destruction of Earth was prevented, an energy source in the form of a spiral was created very close near Enoch's spaceship. The Chronicom apologised to Fitz for the situation, trying to estimate his chances of survival. He looked at the spiral through a window, as it suddenly got bigger and cut the ship in two.
One year later, Daisy Johnson, Jemma Simmons, Piper and Davis were being chased down by the Confederacy and were forced to land Zephyr One on D'Rill. One D'Rillian named Trok intercepted them and asked for their permission to land. Johnson choose to confront them alone, pretending that the ship had run out of fuel, and the D'Rillians soon discovered that she was actually Quake. Johnson used her powers to destroy the D'Rillians' weapons, which made them flee in fear. However, Trok attempted to attack Quake and was quickly defeated and thrown to the ground. Jemma came and threatened the D'Rillian, saying that the they were looking for someone who they wanted to bring back to Earth.
Meanwhile, at the Lighthouse from Earth, several S.H.I.E.L.D. agents, including the director, Alphonso Mackenzie, were searching for signals of paranormal activities on an electronic world map. Mackenzie ordered the four STRIKE teams to be on position. Soon, the signal goes off and Fox traces it to Indiana. Being the closest to the location, the team consisting of Melinda May and Keller goes to investigate.
In a park nearby, a group of teenagers were playing basketball, when anomalies began to happen, such as their ball breaking like glass and bat-like creatures rising from a portal. A portal opened in wall and Jaco came out of it, scaring the boys, who ran away in fear. Another portal opened in the same wall and Tinker came halfway through it, reaching his hand for Jaco. However, the portal closed immediately and most of Tinker's body turned to stone. Jaco mourned silently for his fallen friend before S.H.I.E.L.D. came and he was asked to surrender. He simply shot the Quinjet and walked away. The plane crashed, but fortunately no one was killed.
The agents returned to the Lighthouse, where they were scolded by Mackenzie for their failure. They ended up agreeing that they would engage from the ground the next them when they would face "reality warps", as Fox suggested calling them. Keller then came up with the theory that the locations where anomalies formed were the same as the Ley lines, which would help them narrow their search. Mackenzie accepted the idea and told Yo-Yo to go and train with May, while he would do his daily check-in.
Mackenzie went into his office and turned on a hologram of Phil Coulson from the Toolbox. The hologram told him to take problems one step at a time, before Mackenzie was interrupted by May. She praised him for his leadership position, stating that Coulson would be proud of him. He then tanked her for the people she had recruited in S.H.I.E.L.D., and reminded her that the organisation was in need of scientists.
Aboard the Zephyr, Jemma and Daisy hung Trok upside down in order to torture him, as the gravity on the ship was greater than the one on the planet. Jemma threathened the D'Rillian by telling him what would happen to his body in those conditions. Trok pretended not to know anything about the Chronicom Vessel, but eventually gave up and revealed that he bought half of the spaceship.
Mack reluctantly meets Dr. Marcus Benson at a bar who appears to be equally as reluctant to assist SHIELD, but after hearing about the connections to unknown energy sources and deep space, the team manages to pique his interest enough for him to join them. Dr. Benson examines Tinker, who remained trapped inside the wall after his portal incident. Tinker suddenly reacts for a few seconds before transforming even further into stone. However, his movement was enough to dislodge a device from his pocket. The device appears to contain a location and time for the occurrence of the next anomaly, pointing to the Museum of Natural History in Indiana.
The team converges at the given location and waits for the anomaly, however, they are distracted when one of the people inducing the anomalies pretends to be an innocent bystander in need of help. Before the S.H.I.E.L.D. team can react, Jaco and team proceed to destroy the museum just before a mysterious man driving a large truck appears in the middle of the road through the expected anomaly. Agent Fox is shot and killed during the confrontation. While the rest of the team is temporarily incapacitated, the mysterious group escapes. May notices that the man looks exactly like Phil Coulson.