Sine Mora features two plots running at different points in time. The first features a father bent on taking revenge on the Empire that executed his son for being the sole pilot that refused to drop a nuclear bomb during an attack on the Enkies. The second features the last survivors of the Enkie race also plotting revenge on the Empire for destroying them. The game stages are often set at the same locations, in noticeably different states due to being set in different eras.
The game takes place on the planet of Seol, which is much like Earth. It differs in that its crust is so unstable it often causes quakes that radically reshape its geography in a small amount of time. Albeit originally split into four great nations, by the time the plot unfolds two factions are locked in the Eternal War: the aggressive and dictatorial Layil Empire and the Atarach Kingdom of the Enkie race. Following the teachings of the great prophet Enki, the Enkie are renowned for their unique talent of manipulating time, to the point of being able to transport any item or even themselves to any point into the past or even the future. Over time, however, the Empire develops “The Project”, a machine capable of manipulating time. The apparatus is capable of arbitrarily accelerating an item’s or even living being’s time flow to the point of literally erasing it from existence. Stored inside the floating fortress-city of Siriad, the Project uses every military vehicle of the Layil as a relay, creating a weapon that cannot be effectively disabled. This advantage has allowed the Empire to cut through Enkie defenses, culminating in a vicious (presumably) nuclear bombardment of the Atarach kingdom.
In the “normal” narrative, which encompasses the player’s first playthrough, Ronotra Koss is mourning the death of his son, Argus Pytel, at the hands of his crewmates as he refused, during the flight of the bomber Cobalt King, to drop a nuclear bomb upon the Enkie capital city; embittered and vengeful, Koss mans a stolen Sine Mora school “Merenstein” plane and, with the help of a smuggled combat artificial intelligence, GARAI 74/22876, starts to systematically infiltrate Layil Empire structures and eliminate officers involved with his son’s demise, all the while exacting a bloody revenge on the Empire which abandoned him after an incident left him an amputee. Finally reaching the city of Tira, capital of the Empire, he mercilessly destroys most of its military force, finally facing the colossal Domus assault fortress manned by the officer who killed Argus, managing to destroy it after maneuvering through its defenses and blowing up the power cores.