The first big antagonist of Digimon Savers was Merukimon, who held a grudge against humans. It turns out, however, his hatred for humans was well-founded, and his heart was not so black after all.
Akihiro Kurata was the true villain of the piece. He was part of an expedition to the Digital World which was misconstrued as an invasion. His fear of Digimon lead him to attack them mercilessly and he would go on to attempt a full-on genocide against Digimon, leading his army of IDF soldiers artificial Digimon called Gizmon on a sickening march through the Digital World using weapons devised to fully erase Digimon from existence so they could never be reborn. He later used that data to not only awaken the Great Demon Lord Belphemon in an attempt to push humans and Digimon further into war, but to also merge himself with it so he could maintain control over it.
Kurata presumably died after he attempted to suicide bomb reality itself, causing the Digital World and human world to literally collide as the walls between worlds shattered.
He was a perfect villain - he was very hateable, and very believable because there are real people like him out there in the world today. I hate him like Harry Potter fans hate Umbridge, except he's from a more well-written piece of children's media.
