This show was an animated action show. It seems it was an American anime.
In one of the episodes, the bad characters were trying to attack the good guys from their headquarters, so they started flying a drone around the wasteland, and the guy flying was some goon, and he thought it was a simulator and started shooting at his HQ, and accidentally blew it up or damaged it badly.
In another episode, maybe the same episode, two good guys walking through the land, I believe the scenery was like the Grand Canyon. One guy says to the other while walking something along the lines of "Yea, but I was raised by him, he was evil" and the guy he said that to, replied, "Yea but you know the difference between right and wrong."
This show was in English on VHS tape if that helps and I may have watched it in 2006 or 2007. It probably wasn't widely known.