Yamaki would often track Wild Ones as they bio-emerged. He viewed Digimon as a threat and wanted to destroy them all. He sometimes watched the tamers as they battled Wild Ones, thinking them to be "playing a dangerous game". When a failed experiment caused a digital zone to appear, Yamaki developed a program called Yuggoth and destroyed the digital zone. After the fight with Musyamon (who countered Yuggoth), he introduced himself to Takato and Henry, voicing his opinions to them, and Henry chased after him, but lost him.
Eventually Yamaki captured a Wild One, DarkLizardmon, and considered taking Guilmon as well. He had his scientists scan DarkLizardmon to find out how Digimon could be destroyed. DarkLizardmon was killed in the process. Yamaki then got permission from the guys upstairs to test his new program, Juggernaut, which would suck Digimon into a black hole and destroy them.
However, this had the side effect of opening a portal through which Mihiramon, the first of twelve Devas, came through. Yamaki lost his mind and blamed the tamers, even though what happened was his fault. When WarGrowlmon destroyed Mihiramon, Yamaki couldn't believe it, removing his sunglasses for the second time and saying maybe the tamers weren't playing some game after all.
After gathering the Monster Makers together, Yamaki decided to destroy all Digimon with Juggernaut during Vikaralamon's attack. Janyu opposed this, as it would destroy the tamers' Digimon as well, but Yamaki insisted that it needed to be done. However, Makuramon destroyed the Juggernaut vortex, causing much of the Hypnos equipment to collapse. Yamaki remained inside the building, but survived.
Yamaki was fired after this incident, and from here decided to help the tamers rather than hinder them. As they were about to go to the digital world, he gave them a com device so they could keep in touch.
When government agents restarted Hypnos without Yamaki, and then did a test run of Juggernaut, a non-corrupt agent called Yamaki, who shut Juggernaut down when the others couldn't.
Yamaki appeared at the building where the tamers' parents and Monster Makers were present. Janyu didn't trust him at first, until watching him communicate with Takato and Henry on the com device. Yamaki was also present at the Hypnos building when the tamers and their Digimon traveled back to Earth on an ark.
Yamaki also watched the battles against the D-Reaper, telling the military that they couldn't defeat it and that the tamers were doing better than them. He also received a message from the ark, which he and the Monster Makers remodeled into an armored form called Grani.
Yamaki also switched Locomon's train tracks to send him back to the digital world.
- Yamaki looks similar in appearance to T.K. from the first two seasons, leading some to believe that he is him, even though this is a separate universe.
- Of the five main antagonists (Yamaki, Zhuqiaomon, Mephistomon, D-Reaper, and Parasimon) Yamaki is the only human. He is also one of the only two to turn good and survive, other being Zhuqiaomon.
- Yamaki's reasons for wanting to destroy Digimon are similar to Zhuqiaomon's reasons for wanting to destroy humans.
- Yamaki removes his sunglasses a total of six times in the series.
- Until the seventh episode, his face is never clearly seen, aside from small shots of his mouth or the eye of one of his sunglasses, most of the time his face is either out of view or the shot is the back of his head. This gives him resemblance to the James Bond villain Ernst Stavro Blofeld, with his lighter acting in a similar way to Blofeld's cat.