Gears of War 3 begins as Chairman Prescott unexpectedly arrives on the Sovereign. Prescott informs Marcus Fenix he needs to relay important information to the ship's senior officer, Captain Michaelson. The Lambent then launch a surprise attack on the ship, which leaves Michaelson dead and Prescott mortally wounded. Before dying, Prescott gives Marcus an encryption to the disc that Colonel Hoffman has and reveals that his father, Adam Fenix, is still alive but captive on Azura, a secret COG base. Marcus, Dom, Cole, and Baird fight their way to the Anvil Gate Fortress, where Hoffman possesses the necessary equipment to decrypt Prescott's disc. Upon arriving at Anvil Gate, Marcus and his comrades assist Hoffman's soldiers in repelling a combined Lambent and Locust assault.
Upon further analysis of the disc's content, Marcus learns that Azura is protected by man-made hurricane generators, making the island only accessible by submarine. Marcus and his comrades, joined by old friend Dizzy Wallin, successfully find a submarine but require Imulsion to fuel it. Dom suggests they first venture to an abandoned town called Mercy, where they discover that humans are becoming Lambent. During extraction, the Gears are nearly overrun by Locust and Lambent; Dom sacrifices himself to create an explosion that wipes out the hostile forces. Demoralized, they are forced to continue their search for fuel in the city of Char after their truck runs out of fuel. The ruined city is inhabited by several Stranded civilians who are led by Griffin (voiced by Ice-T). Despite his dislike for the COG and Gears, Griffin reluctantly tasks Marcus to recover a supply of Imulsion. After acquiring the fuel they are attacked by the Locust Horde, led by Queen Myrrah. Griffin's forces sustain heavy casualties in the ensuing battle, but the Gears are ultimately able to escape and reach the shipyards where they have to fight the Locust as they repair and fuel their submarine.
Marcus' group finally arrives at Azura, discovering that it is a sanctuary and resort for Sera's most elite and powerful individuals. Adam contacts the Gears and reveals he is being held captive atop Azura's main hotel tower. Marcus's group battles through waves of hostiles before finding his father. Adam quickly explains that he has created a device capable of eradicating all Lambent and Locust life forms on Sera. Adam had worked with Myrrah before to try to tune the wave so that only Lambent would be affected, but with the Imulsion, revealed to be a parasitic lifeform, now infecting humans, Adam ran out of time, infuriating Myrrah. Marcus and his comrades defend Adam from the Locust and Lambent, and from an attack by Myrrah. Adam reveals that he had to infect himself with Lambent cells in order to test his machine. As the machine begins to pulsate with energy, Adam bids his son farewell before the device kills him. Myrrah rises from the rubble and begins insulting Adam. Marcus fatally stabs Myrrah with Dom's commando knife he got back in Mercy. Shortly afterwards, the machine emits a blue wave of energy that sweeps across Sera, destroying the Locust, Lambent, and the Imulsion. The scene transitions back to Marcus, who is mournfully wondering what humanity has left. He is comforted by Anya, who assures Marcus that the sacrifices of Adam, Dom, and their comrades have guaranteed humanity a future.

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