After monitoring and unsuccessfully trying to destroy a few Wild Ones, they captured DarkLizardmon, scanned (and destroyed) her to find out how Digimon could be destroyed, and developed the program Juggernaut. However this only opened a portal for the Devas to attack.
When Makuramon threw a Primal Orb into the void of Juggernaut, Hypnos was shut down, all their equipment destroyed or damaged. Yamaki and the other members of Hypnos decided to help the tamers from this point forward.
Government agents restarted Hypnos without Yamaki, as well as Juggernaut, but one of the agents who opposed this brought Yamaki in and he shut Juggernaut down.