Charybdis was an Ancient experiment created by Janus and his protégé, the child prodigy Ikaros, intended to erase the Iratus Bug from history, and thus prevent the evolution of the Wraith. Established on a planet known as Mykena Quattuor, the equipment that would activate Charybdis was activated when the Atlantis expedition discovered Ikaros, who had downloaded himself into a quantum computer of his own design so that he could ‘do the math’ and calculate how to create a timeline that would erase the bug while not erasing Atlantis itself. Charybdis itself possessed a certain level of sentience to correctly establish the resulting timelines.
Unfortunately, even when Ikaros was able to create timelines where Atlantis would still exist while the Wraith were erased, Charybdis still resulted in multiple dystopias created due to the lack of the Wraith depriving the Ancients of their reason to advance while maintaining their morality, including;
Charybdis +32: A world where the activation of Charybdis had destabilized the Stargate network and destroyed Lantea, leaving only the Athosians and a few other survivors - including the original Teyla Emmagan, apparently blinded in the catastrophe - to make a life for themselves around Atlantis’ remains which ended up buried on the mainland due to shifting of the planet caused by Charybdis.
Charybdis -4441: A world where Janus and Dr. Elizabeth Weir's plan to save Atlantis ("Before I Sleep") failed when the stasis chambers Elizabeth was using malfunctioned, causing Elizabeth to awaken approximately five thousand years before the expedition would arrive in the city, Elizabeth suffering a mental breakdown from the loneliness and isolation she felt being trapped in Atlantis and unable to operate its systems (The original Major John Sheppard arrived in this world).
Charybdis +4: A world where the survivors of Charybdis had become convinced that Charybdis remained and had developed sentience, willing to destroy any attempt to avert it, the resulting ‘cult’- lead by the alternate Dr. Radek Zelenka and including the original Elizabeth- becoming addicted to the lotus-like flowers of this world out of a lack of anything else to do (Although Elizabeth was able to escape the addiction herself).
Charybdis +13: A world where the Ancients, lacking the Wraith to fight, had become conquerors themselves, enslaving soldiers - including Ronon Dex - using a nanite hive-mind known as the ‘Behemoth’ in their soldiers to discourage and eliminate rebellion.
Charybdis -908: A world where Ikaros was regarded as a virtual devil for the destruction his experiment had caused, research into science being dismissed as heretical and those found researching it - such as the now-teenage Dr. Rodney McKay - sentenced to execution.
Charybdis -223: A world where the Ancients had regressed to a more primitive state and lost most of their scientific knowledge, relying on what they could re-discover in the remains of Atlantis - aided by the original Zelenka - while lacking any real incentive to progress further than what they were already.
Fortunately, the Stargate network, while damaged by the entropy Charybdis had created when it altered history, was still trying to repair itself, allowing the original versions of the original six people present when Charybdis had originally been activated - John Sheppard, Rodney McKay, Elizabeth Weir, Teyla Emmaggan, Ronon Dex, and Radek Zelenka - to find their teammates by travelling through the Stargate with alternate versions of their teammates as the gate matrices attempting to bring the originals together to undo the damage. In extreme cases, the team used the body-parts of their alternate selves to find each other; Teyla found the original Ronon after she took a finger from the body of his counterpart in her world, Ronon subsequently taking the ear of his McKay to find the original, while an alternate Sheppard and the original used an alternate Weir to find the original, with Sheppard and Weir using blood from an alternate Zelenka and McKay, Teyla, McKay and Ronon using the skull of an alternate Sheppard to find everyone else. The activation of Charybdis twisted time to such an extent that even the ages of the survivors were altered, Teyla and Zelenka gaining thirty years while McKay was regressed to a teenager, John Sheppard being the only person to come through Charybdis the age he should be.
With the aid of Ikaros - who had transferred himself into McKay’s mind at the last minute before Charybdis was activated - the Atlantis expedition were able to return to their original timeline moments before Charybdis was activated, Ikaros merging with the rest of himself in the quantum computer and fully Ascension, allowing him to destroy Charybdis and heal the team’s remaining injuries before returning to the past. (Stargate Atlantis: Mirror Mirror)
Charybdis was an ancient sea monster living in the Straits of Messina in Italy, later explained as a whirlpool.