- I found out she's an angel
- I don't think she knows I know
- I'm worried that something might happen to me
- If anyone ever finds out
- —They Might Be Giants, "She's an Angel"
Project Serra is a sinister secret project of some sort which studies superhumans. It has ties to the orphanage where Particle Man grew up. While Particle Man escaped their clutches, his former girlfriend Lucky Ball and Chain was not so, well, lucky, and the Project transformed her into an angelic superbeing under their control. They also created a number of Particle Man clones.
When Particle Man returned to the orphanage seeking more information about his history and powers, Lucky captured him and took him to the Project, where he was imprisoned and experimented on for a month. With Blue Canary's help he broke out, destroying the Project and killing most of its employees and experiments. But a few (including Lucky) survived, and plotted vengeance on Particle Man.
They assembled the handful of surviving clones of Particle Man--the energy being Photon Man, the cybernetic Particle Borg and the teenage Particle Kid--together with the vengeance-driven engineer John Henry as the Particle Men to kill him. Particle Kid and Particle Borg broke free of their control and defeated the others; John Henry was the only survivor.
After this, John Henry and the other remaining members of Project Serra began an extremely complicated plot (chronicled in Birds Fly) to incapacitate Particle Man, Drifter and Occultism Kid using statues infused with the TheyMightBePowers; Blue Canary and Windrider teamed up to oppose them. Unfortunately, the story was never finished so we'll never know how all that turned out.
The organization is named after the Serra Angel from Magic: the Gathering, naturally.