1. Missing Pieces

A year after the death of director Phil Coulson, S.H.I.E.L.D. is rebuilding under the leadership of Alphonso "Mack" Mackenzie. They investigate a series of energy anomalies formed by hostile strangers emerging from portals, one of whom gets trapped inside a wall and partially turns to concrete. In deep space, Agents Daisy Johnson, Jemma Simmons, Piper, and Davis search for Leo Fitz, who was last seen in a cryofreeze chamber on a spaceship with the Chronicom Enoch; they find the spaceship abandoned and the chamber empty.

Simmons learns that the chamber was created on Naro-Atzia, but the others decide to return to Earth. They are attacked by a Confederacy cruiser and, in the rush to escape, Simmons plots a course to Naro-Atzia. Mack and Melinda May recruit Dr. Marcus Benson to help found a S.H.I.E.L.D. academy and provide science support. They find coordinates on the man in concrete, Tinker, which lead them to a museum. The surviving hostiles are there and destroy the building to make way for their leader, Sarge, who looks just like Coulson.