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In the events following Invasion, Colonel Johnny Rico is assigned to train a new group of troopers on a Martian satellite. However, these latest recruits, being Martians themselves, show a lackluster attitude toward the war effort, considering it irrelevant because their planet has remained untouched by the bug invasions. In general, Mars displays minimal enthusiasm for continuing the fight, with some even advocating for withdrawal from the conflict. This complacency leads to a devastating surprise when the bugs launch a sudden attack. Meanwhile, unbeknownst to everyone, Sky Marshal Amy Snapp is secretly executing plans to seize control.

Invasion starts with the Bugs launching an attack on Fort Casey, a Federation outpost. The fast attack ship Alesia is dispatched to assist the starship John A. Warden, currently stationed at Fort Casey, in evacuating survivors and delivering vital military intelligence to Earth. At the same time, Carl Jenkins, the head of the Ministry of Paranormal Warfare, takes the starship on a secret mission before rendezvousing with the Alesia, then vanishes into a nearby nebula. The veteran troopers are subsequently given a rescue mission that may lead to repercussions far darker than they ever anticipated.

Appleseed Alpha tells a self-contained story that stands apart from the original Appleseed film continuity, yet it comes from the same director. In this iteration, Briareos is already a cyborg from the start, and shares no prior history with Deunan Knute before the two of them join ESWAT in Olympus. The plot focuses on the early journey of Deunan and Briareos in the 22nd century, as they navigate the devastated landscape of New York, attempting to reach the ideal city of Olympus. Two Horns, the ruler of this ruined metropolis, contracts them to destroy bipedal war machines. During their task, they cross paths with Iris and Olson, who are carrying out their own agenda. After forging a connection, Deunan and Briareos decide to support Iris and Olson. Iris's mission is to stop the sinister cyborg Talos from obtaining a concealed human weapon. However, Talos deceives Iris into activating the colossal war machine.