Hypnos

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Hypnos's original purpose was to monitor electronic communications of half the Earth for the Japanese government. Because of the legal issues of violating privacy, Hypnos was kept secret from the public. However, Hypnos discovered Digimon (termed "Wild Ones") who entered the real world. As a result, the agency's new objective is to detect Digimon when they Bio-Emerge in the real world and to prevent it if possible. If a Digimon does manage to cross over, Hypnos would try to capture the Wild One and study it. Another function of the agency is to prevent media leaks about Digimon, as well as cover up incidents (such as creating cover stories) that involve Digimon. Apparently Mitsuo Yamaki, the head of Hypnos, had an agenda to eliminate Digimon once and for all.

However, their efforts at first prove unsuccessful. As time went on, they develop new and better methods of attacking Digimon, but these techniques are ineffective against the Deva. In their efforts to better understand and defeat the Digimon, Hypnos recruits the computer programmers who originally made the Digimon, the Monster Makers, and attempts to use their knowledge to create a successful anti-Digimon weapon.

After the Tamers enter the Digital World, Hypnos's objectives change: they now seek only to bring the kids home. This new realization comes after Hypnos's leadership realizes that not all the Digimon are evil. Eventually, their efforts allow the children and their Digimon to return to the Real World. Hypnos later helps in the battle against the D-Reaper by providing space and technology.

Hypnos is covertly headquartered in the Tokyo Metropolitan Government Building, which also houses the Hypnos computer system, as well as several labs for research. The agency employs scientists, operators, and computer programmers, as well as several field agents. Also at Hypnos's disposal are unmarked black vans and helicopters, used for investigation and combating Digimon. Since Hypnos is a government agency, Yamaki reports to four officials, presumably his superiors in the Japanese government, and to the Chief Cabinet Secretary.

In the aftermath of the D-Reaper incident, Hypnos changes its views on how to deal with Wild One appearances. Specifically, they turn to tamers to fulfill a job that they are best suited for.

Yuggoth
Essentially a blast of virtual energy, the Yuggoth program locks onto and strikes Digimon, supposedly deleting them. But, in some cases, the Digimon who is bio-emerging is able to withstand and disable Yuggoth temporarily. The Yuggoth program is later downloaded into Gallantmon's vehicle Grani.

Juggernaut
The Juggernaut program is most powerful of Hypnos' weapons. It is a digital vortex that draws in all data nearby, including Digimon. The program nearly succeeds in destroying many Digimon but inadvertently allows the Deva Mihiramon to pass into the human world. The Juggernaut's subsequent uses are equally ineffective, until it is downloaded into Terriermon. As MegaGargomon, he and his partner Henry Wong use it as part of Operation Doodlebug. It regresses the D-Reaper back to its original harmless state by reversing the flow of the D-Reaper's vortex to create a reverse time effect and causing a minature big bang, in Yamaki's words, in the D-Reaper's quantum bubble, which causes the D-Reaper to get sucked in and reverted by the reverse time flow.

Ark Program
A transport program created by Hypnos with the Monster Makers' help, the Ark's purpose is to bring the Tamers home from the Digital World. However, the program evolves beyond its original purpose and develops intelligence. Later, when the Tamers and their Digimon are locked in battle with the D-Reaper, Hypnos recovers and modifies the Ark into an attack vehicle, and attempts to materialize it in the human world. However, it is unsuccessful until Gallantmon channels his energy into it, creating Grani.