The main story is that of Leonard and Pearl Hohenberger who are genetical engineers/scientists and their son Joseph.
Wilhelm Ryan, a Mage, begins a war against the other Mages so he can claim the title Supreme Trimage, and rule over all of the Keywork.
While attending a peace rally Joseph is killed by Ryan's forces.
Leonard wants revenge, and sets out to create soldiers capable of helping this cause.
Inferno, Coheed, and Cambria are created.
They are sent out on various guerrilla missions, and become known as the KBI (Knowledge-Cambria, Beast-Coheed, and Inferno)
Wilhelm Ryan learns of their origins and sends General Deftinwolf to the Hohenberger's house. He tells Leonard that Pearl is being held hostage until Leonard turns over Coheed and Cambria, and completes a deadly virus (Monstar) that will wipe out all the life on the Keywork.
Leonard eventually accepts this as the only way to get his wife back and completes the virus, but to ensure it is not used immediately he uses a code word to render C&C unconscious and imparts part of the Monstar virus to each, so that it will take time to reconstruct. Additionally he starts another person growing, Josephine, named after his son, who will have antibodies that can be used to cure the virus. Pearl is returned to him and Ryan takes C&C back to House Atlantic.
Upon finding out what he did to save her Pearl becomes distraught and kills herself at her son's grave. Leonard, seeing that he has nothing to live for, attempts to kill Deftinwolf and is killed.
Inferno finds a message from Leonard that tells him about the plan to make a cure, but he realizes that due to genetic modification it will be in excess of 20 years before Josephine can produce a cure.
He sets out to rescue C&C, and brings them back, where he then speaks the code word, and essentially reprograms them to forget all that had happened and to think they were normal people with their daughter Josephine.
and that's the gist of it, although its a lot more fleshed out obviously in the book