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Weed's a mystery for almost the whole trilogy. At first he's just a nerdy kid in the academy. Then we find out he's the son of Cygnus members. Then we find out he's working for Willux and has brain enhancements. Then he's the lead doctor in the Dome.
So really, we have no idea what side Weed is on: he's either really good, or really evil. But one thing's for sure: Weed might just be the most powerful man is the trilogy.
Weed has the ability to make people. Yeah, he's that smart. But that also means he has the ability to reverse the effects of the Detonations, as well as Rapid Cell Degeneration (which, by the way, he suffers from because of the brain enhancements).
Oftentimes he winks at Partridge, but we don't know if that's and evil wink or a good wink. He also speaks in code too; but he's so smart, and might just be tricking Partridge. In the end though, we find out what side he's really on:
His voice is choked by sadness. He coughs and says, "Willux made me create them. Now it's my responsibility to keep them alive." (59.79)
Yep, Weed's been a good guy all along. And just like many of the other characters, his driving force is revenge. He wants revenge for his parents and little sister. He might just be one of the bravest people in the Dome, and the savviest: the only way he can make things right is to make them initially wrong.
Weed's not just some nerd; he's the one guy that could act as the savior of civilization.