In 2183, the human colony of Fehl Prime, a major producer of pharmaceuticals for the Systems Alliance, comes under a brutal assault from Blood Pack mercenaries led by the krogan Archuk. In response, the Alliance sends several Marine units to help, but only one squad survives the shuttle’s crash: the stalwart Delta Squad. Lieutenant James Vega steps up to lead after Captain Toni is incapacitated, and he is joined by a tight-knit group of fighters: Kamille, Nicky, Milque, Essex, and Mason. Together they press forward, determined to halt Archuk’s momentum, and Vega proves his leadership by taking down Archuk and capturing Archuk’s second-in-command, Brood. In the aftermath, Admiral Hackett orders Delta Squad to defend Fehl Prime against future assaults.
Fast forward to 2185, Fehl Prime has begun to recover, and the Alliance has bolstered its defenses with a heavy anti-ship cannon and advanced kinetic barriers. As the squad helps install these defenses, they uncover an enigmatic alien device emitting a signal. Treeya presents her findings to Dr. Liara T'Soni(/actor/jamie-marchi), but communications are quickly jammed when Liara speculates the device could be linked to Reaper tech. While returning to the colony, the team spots a looming invasion: a Collector ship descends, releasing Seeker Swarms that cripple the colonists and even touch Captain Toni.
Desperate, Delta Squad attempts to disable the Collector ship with the colony’s cannon, but the weapon is destroyed. The team retreats to the underground labs beneath Fehl Prime, where chaos erupts as Kamille is ripped away by drones and Essex is paralyzed while defending the lab doors. Inside the labs, Delta Squad uncovers that Messner is actually a Cerberus double agent trying to access the facility, and they discover a possible antidote to the Seeker Swarm’s paralysis. The group also finds Brood kept in a tank as a test subject. The defense collapses when a Praetorian tears open the doors, incorporating Kamille’s body into a horrific attack; Mason dies while trying to rescue her, and Delta Squad is forced to retreat with Brood.
Brood leads Delta Squad to his hidden ship as repayment for Vega’s help, and they lift off just as the Praetorian returns with fury. The chase ends with Nicky being killed, a brutal blow to the squad. Vega orders a bold frontal assault on the Collector ship and manages to board it, but Messner murders Brood, leaving Delta Squad captured once again.
In orbit, the Collector ship scorches Fehl Prime from space. Messner explains to Treeya that he planted the alien device to draw in the Collectors so Cerberus could seize their technology, and he drags Treeya with him deeper into the ship. Vega, Essex, and Milque are sealed in pods, but a drink Vega had given everyone earlier—spiked with the Seeker Swarm antidote—enables them to break free and eliminate their guards. The trio pursues Messner and Treeya as Milque secures transport to escape.
Meanwhile, Messner unveils a Prothean archive embedded in the Collector vessel and forces Treeya to access it. Treeya witnesses footage of the Protheans’ final stand against the Reapers, their transformation into the Collectors, and the creation of a human-shaped Reaper on their homeworld. Messner records this intel on his bracelet, only to be betrayed by the Collectors. Treeya steals the bracelet and escapes in a containment pod.
Vega and Essex press on to confront the Collectors, destroying their forces and damaging the ship’s controls. Essex is fatally impaled by the ship’s claw, but uses his biotics to hurl both of them into a chasm, where they fall to their deaths. Messner fires on Vega, who disarms him and stabs him in the stomach, leaving Messner to die in a ship-wide explosion. Vega learns that Treeya holds the essential intel, and, faced with the choice between evacuating the colonists on a compromised ship or saving Treeya and the data, Vega chooses Treeya. As Treeya’s pod is recovered, the Collector ship crashes into Fehl Prime’s surface and detonates, killing Captain Toni and most of the colonists and leaving Vega, Milque, and Treeya as the lone survivors.
Back on the Citadel, Vega is commended by Captain David Anderson and Admiral Hackett for the crucial intel he preserved, and they reveal that Commander Shepard is alive. They present him with a petition to join the N7 program, signaling a new path forward. Some time later, the trio returns to Fehl Prime to mourn the fallen; Vega experiences a breakdown upon discovering April’s doll, and he leaves April’s dirtied badge and doll at a memorial as the survivors pay tribute. In the end, Vega leads a squad into battle once more, vowing to keep fighting in memory of April, Toni, and all the colonists they could not save, carrying their memories into every future engagement.