- "Rubicon is Darhk's flood."
- —Oliver Queen on Rubicon and Project Genesis[src]
Rubicon was created as a fail-safe against nuclear Armageddon. It consisted of a program and a device that stored it. The device was originally stored in A.R.G.U.S. headquarters, until Shadowspire tried to steal it. For safety purposes, the device was placed under director Lyla Michaels's skin in the form of a subdermal implant.
Rubicon was designed to be "unhackable", using Fourier protocols to ensure its security. Rubicon would also know whether the missiles would launch or not, worldwide. In case of a security break, the program would continue trying to send launch codes to all nuclear missiles, one by one, whether to deactivate them or, after being reprogrammed by H.I.V.E., to ensure the launch's success.
Rubicon was part of Damien Darhk's plan to ensure the nuclear devastation of the whole planet, leaving H.I.V.E. as the only force capable of rebuilding it and "starting life anew", with their chosen people safely surviving the nuclear annihilation in Tevat Noah. Using his dark powers, the terrorist leader ripped the subdermal implant from under Lyla's skin and brought it back to his organization. H.I.V.E.'s scientists managed to reprogram Rubicon, so that instead of deactivating nuclear weapons, it would launch them on targets all across the world, including the metropolis of Monument Point and its suburb, Havenrock.
Lyla contacted Team Arrow to help stop Darhk's plan. Felicity Smoak and her father, Noah Kuttler, were instrumental in shutting down Rubicon, however, due to the program's ability to recognize the error and send launch codes one by one, a single nuclear missile was launched from Russia that destroyed the town of Havenrock, with tens of thousands casualties, that ended up fueling Damien Darhk's dark magic abilities, making him impervious to Green Arrow's attacks, unless heavily weakened by the Light of the Soul.
Although Felicity Smoak and Noah Kuttler managed to develop the program to counteract Rubicon, the laptop to which it was uploaded was stolen by Damien Darhk during his visit to Smoak's place. Subsequently, Darhk entrusted Cooper Seldon with restoring control over Rubicon and launching the nuclear missiles once again, threatening to painfully kill him with dark magic in case Seldon does not comply. Felicity convinced Seldon to sacrifice himself and save the world, taking control of Rubicon once again and making sure none of the launched missiles finds its target. 
Behind the scenes
- The idiom "crossing the Rubicon" means passing a point of no return, and refers to Julius Caesar's army's crossing of the Rubicon river (in the north of Italy) in 49 BC, which was considered an act of insurrection and treason against the Senate of the Roman Republic. Julius Caesar uttered the famous phrase "alea iacta est" (the die is cast) as his army marched through the river. In this case, Rubicon refers to the event of nuclear war, in which A.R.G.U.S. would use the device to deactivate all nuclear weaponry on the planet.