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The story of DNA Wars is centered around a male clone named Romeo Dantes, who works, like most clones, in construction. He's especially prized by his master, however, because he's a very clever architect, a real genius for designing buildings. Of course, he's just a clone, so that doesn't mean he gets paid or anything!

Not that he wants to; Romeo enjoys his simple life and his simple possessions, a tiny room (while most clones sleep in multi-layered bunks) which he especially appreciates because it allows him to keep safe his sole prized possession, a black kitten named Wiki.

His simple life becomes rather more advanced one day when some Master-Race teenagers begin abusing Romeo at the market-place, threatening to beat him because he refused to hand over Wiki. Just as the boys begin to close in, Romeo's saved by Jessica, a young master race girl, who says she'll inform Romeo's supervisor (a rich and powerful man) that they were interfering with his prized clone. The boys reluctantly subside and leave Romeo and Jessica alone.

Jessica is not rich by any means, the daughter of a small-time grocer, though she has a large heart and a kind spirit. Also a big brother, which no doubt was quite helpful when she saved Romeo. She and her brother are members of the Abolitionist Group, those who believe that clones should be set free, a viewpoint which she thinks Romeo will be quick to adopt. Mistakenly, as it turns out. Romeo is loyal and basically happy and sees no reason to complicate all that with freedom, even as he falls in love with Jessica. A love which she returns but must be kept utterly secret: human-clone relations are punishable by death (for the clone anyway).

Casting each other long glances and meeting in secret gardens to steal kisses, they live a dangerous life, knowing they should stop but neither willing to be the one to end their love. Until, as must be the case, they are caught. Romeo is thrown in jail, slated for execution. Jessica pleads for his life, and her pleading is easily ignored.

But then the inevitable happens. On the day of Romeo's execution, the clones finally rise up in full rebellion, lead by the rare soldier clone Voldemon #7 and his secret group: the Black Hearts. They invade the prison, rescuing their many companions and freeing Romeo too. When asked whether he will join the fight (at gunpoint), he says yes, but then finds the first moment to sneak away, rushing headlong through a great civil war to find Jessica and keep her safe...