Q:

90s sci-fi series with an episode where a boy goes into VR and fights a Medusa-like monster

I am looking for an animated series, shown in the 90s. I remember an episode where the boy went into VR and fought a medusa-like monster. 
It may be that this was the premise for the whole series: That the children heroes go into VR every time to fight the evil guys. 
I am not sure if the whole series were computer-animated but surely there were such elements together with classic animation.
The style of the series was quite dark and cool for teenage boys.

A:

I suspect you're thinking of the "Heroes" episode (Season 1, Episode 18) of The Real Adventures of Johnny Quest. Questworld, a VR simulation, was a common plot point, and that episode included a Medusa.

Medusa scene

