Early Reins features six beautiful women on a train en route to Sunshine Hill in the early 1800s. When the train is highjacked by robbers and the soldiers on board are caught unawares, another surprise is in store: these lovely ladies can fight! The heroine emerges as Margarette, a young woman determined to become a sheriff although she is somewhat lacking in experience. She gains plenty on this trip, however, and the ragtag team of Western warriors joins forces with another passenger, Spencer, to fight some nefarious bandits and guide the train to safety.

Following the destruction of the magical floating device from OVA 1, the Magic Academy falls to earth, but unfortunately lands on and breaks a demon seal, releasing hundreds of ancient demons into the forest around the academy. The teachers are barely keeping the demons away and are desperately searching for the pieces of the floating device, so to earn more magic stones, all of the students from Amelia's class decide to leave the academy (even though they were told not to) to find the missing pieces.

Even though the Decepticons have been driven off Earth, a small team of Autobot Pretenders have remained behind, just in case. Led by Metalhawk ("Hawk" in his human identity), the Pretenders live among the humans, using their Pretender shells to assume human size and appearance. The Autobots' caution is rewarded: Decepticon Pretenders soon appear, led by a mysterious force called Devil Z. The Autobots and Decepticons soon build up their forces, recruiting humans to become Junior Headmasters and Godmasters (Powermasters).

On August 10 2002, the eruption of Mount Fuji, as well as a series of large-scale earthquakes tsunamis inflict tremendous damage to Japan, sending the country into a state of emergency. Furthermore, another massive earthquake hit Japan on August 15, splitting the country into two. While Japanese refugees were taken in by various countries, the Japanese government accepted aid from China and the United States, which eventually caused China to govern the North, and the USA to govern the South. 15 years later, the Japanese refugees residing in Taiwan and the Taiwanese citizens find themselves clashing with one another, due to job competition and the unimproving conditions of the Japanese refugees. Genichiro Ryu is a survivor of the catastrophic events that took place in Japan, but was raised in Taiwan by a couple who adopted him. He gets himself involved in the situation between the Taiwanese and the Japanese, hoping that the two parties will be able to coexist with one another.