The boss known as Alpha.EXE or Alpha Virus, is the main enemy in Mega Man Battle Network 3.
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Alpha was originally not a virus, but a network. It was an "Alpha" version of the internet that Lan and MegaMan.EXE know so well today. It was created by his grandfather, Doctor Tadashi Hikari. However, Alpha became corrupted by viruses and somehow became a sentient virus itself. It had the potential to destroy the entire cyber world. Because of this, it was locked away. Instead of just, you know, smashing the hard drive.
Of course, whenever there's a hidden super destructive weapon, some bad guys going to make it his goal to resurrect it. Just look at Lavos.