The year is 2010. Shockwave — long resentful of Galvatron's brutal leadership of the Decepticons — discovers the Zel Quartz on the planet Zel Samine, a power source that exceeds even the Heart of Cybertron. He implants it and stages a coup, taking command of the Decepticons — until the overwhelming power overloads his systems. He malfunctions catastrophically, destroying significant portions of both armies, then Cybertron itself, and begins razing other planets.
Unable to stop Shockwave in the present, Rodimus Prime allies with the Quintessons to send an elite team back to 2003 — before Shockwave ever finds the Quartz.
In 2003, both the Autobots and Decepticons detect the arrival of the time travelers above Zel Samine and each dispatch an investigation team. Both vanish. The Autobots send Optimus Prime, Wheeljack, and Jazz as backup; their shuttle crashes. Wheeljack determines that Zel Samine's sun causes electromechanical malfunction and drains power. The Decepticons send Soundwave and Starscream, with Megatron arriving separately via a malfunctioning Space Bridge. Unable to repair their own ship, they steal Autobot energon to get mobile again.
Stranded on the same planet, both factions fight over its power sources — the Mount Jaad wind facility, the Ranpas Geothermal Plant, the Monogan Hydroelectric Station — and begin encountering missing members of their respective reconnaissance teams, along with their future counterparts: Rodimus Prime, Kup, and Arcee from the Autobot side; Galvatron, Cyclonus, and Scourge from the Decepticons. Galvatron tells Megatron he rules the future and that the Zel Quartz is an Autobot doomsday weapon that must be destroyed. He is lying.
Both sides chase down leads on the Quartz's location — the Jewel of Mystery at the Lazalt Ruins, a superhard mineral at the Karzite mine, a crystal formation at the Atalstan gem mine — all dead ends. The planet's central archive eventually identifies a Zel Stone embedded in the ELTA power transmission array as the only match for every description of the Quartz.
A final confrontation at ELTA determines who controls it — but Starscream, having overheard Galvatron and Cyclonus confirm the Quartz's true nature, steals it and flees into space. Without Zel Samine's atmosphere to stabilize its structure, the Quartz degrades immediately and becomes inert. Starscream drifts powerless, exposed to the sun. The future versions of both factions dissolve into light as the timeline shifts. Optimus Prime and Megatron are left to consider what this confrontation has shown them about the future — and each other.