Jonathan Anderson is a young genius in the field of robotics and AI (Artificial Intelligence). Along with his best friend Borland, who specializes in human-machine interfaces, he lands an internship at Peratyn Systems, a leader in robotics development that is heavily funded by government contracts. Jonathan is assigned to the advanced cybernetics software control systems team (Cyber-Con), while Borland is put in the Bio-Mech division where he meets Caroline Decker. Bio-Mech, and Caroline, focus on human biological enhancement, i.e., cyborgs. Also interning at Peratyn is Laura, the girl Jonathan loves. She sees him as a friend, but acknowledges his brilliance.
Jonathan and Caroline face off at their first meeting, each sure their own approach—robots and cyborgs respectively—is the future. Borland is caught between supporting his friend, and falling for Caroline, who is brilliant in her own right, though she, too, suffers under the weight of genius. When bugs in the robot AI delay a key product release, their manager at Peratyn threatens to eliminate Laura's quality control team. To keep her close, and impress her, Jonathan commits to fixing the bugs, with Laura putting herself up as collateral if he can't. As Jonathan's talent is heroically put to the test, it attracts Caroline's attention. She pursues and manipulates him into being with her, blind to Borland's love for her. But, all relationships are tested when Jonathan's new code causes an apocalypse of sorts, and people all over the earth start thinking they are brain-eating zombies.
Jonathan and his team of code monkeys hole up in a shopping mall as they try to figure out what has happened. After being saved by Borland and some cyborgs, the main players go back to Peratyn to figure out how to undo the mess. Different opinions are expressed, and they part ways to work through their respective plans, Jonathan taking a ship to a space platform, Caroline using Peratyn as her cyborg base, and Borland and Laura trying to save humanity with what resources they can cobble together.
Jonathan has left Caroline for Laura, and now thinks Laura has left him for Borland. Caroline has now seen that Borland loved her all along, but she is more machine than human now and he leaves her. His final gift is an artifical heart to replace her failing human heart. Pushed over the edge, Caroline tries to kill Laura. Jonathan thinks she succeeds, making him re-evaluate his life and choices. He goes back down to earth to save Borland from Caroline's wrath, but instead faces it himself. When Caroline chooses not to kill him, and he learns that Laura survived and is on the Space-Y space platform, he goes to rescue her, leaving Borland to save the earth.
The show was written by geeks, for geeks. The dialogue is fast-paced, witty, and filled with technical jargon and nods to geek pop-culture. The music is all by Jonathan Coulton, a programmer turned internet rock star.