Hypnos's original purpose was to monitor the electronic communications of half the Earth as a SIGINT system for the Japanese government. Because of the legal issues of violating privacy, Hypnos was kept secret from the public just as its real-life counterpart project, ECHELON. 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 exterminate 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 powerful Digimon, particularly 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 In their efforts to better understand and defeat the Digimon, Hypnos recruits the computer programmers who originally made the Digimon, the Monster Makers, and attempts to use their knowledge to create a successful anti-Digimon weapon.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 Yamaki (proven to be the only capable manager of Hypnos's systems) realizes that the Tamers need help and that Hypnos thus could be useful. Although at first successful in its endeavor, its mainframe was significantly damaged by the D-Reaper, which could only be solved by a distributed system. Eventually, their efforts allow the children and their Digimon to return to the Real World. However, the D-Reaper soon invades the Hypnos building, forcing the evacuation of technicians and stored memory banks. Hypnos is then progressively relocated further as the D-Reaper expands, but manages to maintain structure and activity.
Hypnos is covertly headquartered in the Tokyo Metropolitan Government Building, which also houses the Hypnos computer system, as well as several labs for research. Hypnos 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 is exposed to the world, and changes its procedures on how to deal with Wild One appearances. One such case is Locomon, whose constant driving around the city causes a massive digital field. Yamaki takes over command of the train office to attempt to redirect Locomon to the digital field and send him home. However, it is revealed that Parasimon is controlling Locomon so he could summon an infinite number of Parasimon to Earth. Luckily, the Tamers are able to stop him and avert the crisis, but not without help from Hypnos.
During their attempts to destroy Digimon, who are composed of data, Hypnos develops two programs meant to serve that purpose. Yuggoth and Shaggai are references to the Cthulhu Mythos, while Juggernaut invokes the raw and indiscriminate power of its namesake.
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.
The Juggernaut (シャッガイ Shaggai?) program is Hypnos's most powerful weapon. 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 Real World. Juggernaut is subsequently upgraded and although at first, it was rather unstable, by the end of the Deva arc it was invulnerable to attacks from the Digital World (due to the Ice Wall the Monster Makers designed). However, it was shut down by an attack from Makuramon, since it came from the human world. When Hypnos is reactivated, Juggernaut is tested out, causing a storm in the Digital World that forces Beelzemon to flee but combined with an attack from Caturamon separates Takato, Henry and Terriermon from the others. Juggernaut goes out of control, but Yamaki and Riley manage to shut it down. In its final incarnation, it is downloaded into Terriermon. As MegaGargomon, he and Henry 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 miniature 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.
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.
- The unspoken irony of Yamaki's situation is that it is possible that the Hypnos system actually created a window, a weak spot, between the Real World and the Digital World, allowing Digimon through in the first place. The series bible sees Chiaki J. Konaka toy around with this idea but it's never fully confirmed as being truth in the finished series – though, at one point, Yamaki does wonder if it could be the case.