ProtoMan.EXE is based on Proto Man from the original series, however the design is notably similar to Zero from the Mega Man X and Zero series (especially his sword-based attacks). Like the original character, both ProtoMan and Chaud carry a lone wolf attitude, take umbrage at help, and are convinced of their superior battle technique.
ProtoMan.EXE is the elite NetNavi of Eugene Chaud (Enzan Ijuuin in Japan). His Navi mark, a circle split with a thunderbolt pattern into two black and white sections, can be seen on ProtoMan's chest and gloves, as well as on the back of Chaud's vest.
Unlike his robot counterpart ProtoMan, he normally uses a sword weapon instead of a buster, although he does carry a shield reminiscent of the original Proto Man's, and does have a buster weapon when he is player-controlled in Mega Man Battle Network 5.
ProtoMan, as a Navi for an official, is extremely well-trained by Chaud, who actually created ProtoMan himself. With ProtoMan's great fighting skills and Chaud's natural talent in NetBattling (or so he says; it was revealed in MegaMan Battle Network 3 that he is not naturally talented, but has trained for 10 hours a day for years), this team is one of the few who can match Lan and MegaMan in strength, even occasionally defeating them.
In the anime, during Axess, Chaud gains the ability to perform Cross Fusion with ProtoMan. When the two find themselves unable to defeat ShadeMan.EXE, Chaud reluctantly provides his Navi with a Dark Chip. In doing so, he released the dark soul in ProtoMan, which allowed him to escape. ProtoMan would later return as Dark ProtoMan (Dark Blues in Japan), a Darkloid completely absorbed by the Dark Aura due to the tampering of LaserMan.EXE. As Axess reached its finale, Chaud was able to rescue his friend's spirit, returning him to normal by Cross Fusing with him, confronting him within the confines of his heart.
ProtoMan.EXE has appeared in all the Mega Man Battle Network games. As a friend and/or rival, Chaud and ProtoMan are always there to help.