Toby Tenma is a teenager who lives in the futuristic city-state Metro City, which floats above the polluted "Surface". Toby's father, Dr. Tenma, is a famous roboticist and head of the Ministry of Science, but has a distant relationship with his son. Dr. Tenma meets the city's obstructive leader President Stone to demonstrate a new defensive robot called the Peacekeeper. To power it, Tenma's friend Dr. Elefun unveils the Blue and Red Core, two energy spheres which have opposing positive and negative energy. Stone has the destructive Red Core placed into the Peacekeeper, causing it to go berserk, leading to Toby being disintegrated after sneaking into the room.
Three thousand years ago, an Aztec warlord named Yaotl and his four generals discover a portal opening into a parallel universe which is said to have great power. Yaotl becomes immortal but at a high price, as his four generals were turned to stone. The portal releases thirteen immortal monsters that destroy his army as well as his enemies. In the present, the Teenage Mutant Ninja Turtles have grown apart. After defeating the Shredder, Master Splinter has sent Leonardo to Central America for training. Donatello works as an IT specialist, Michelangelo works as a birthday party entertainer called Cowabunga Carl and Raphael works at night as a vigilante nicknamed Nightwatcher. April O'Neil operates a company that locates and acquires relics for collectors with the help of her boyfriend, Casey Jones.
The story centers on characters who are immortal.
The lead character, Colin MacLeod, became an Immortal after his first death in 125 AD in Roman Britain, when his village was attacked by the conquering Romans. Another Immortal, Marcus Octavius, was leading the Roman Empire's military forces in hopes of creating his dream of a utopian society. Octavius killed Colin's wife, but was not able to kill Colin whose unconscious body was dragged by a horse to within Stonehenge, a "holy ground" in the story, where Immortals are forbidden to fight.