It is my first time to see this happens. http://pastats.nanodesu.info/chart?gameId=382761 The black commander is unable to be attacked by any weapon. And he can fly between planets. I think he is riding an Astraeus, but the game doesn't display that. And I have tried to bomb him with 5 nukes, it didn't work. Finally, we use Ragnarok to destroy all the planet including ours to finish it. After the game finished, I try to review the replay. But I find I can't even see his commander.
I am not the host, but I am sure the sandbox mode is disable. It is just a regular game, not a special game mod.
This sounds to me like either League of Commanders or Orbital Commander (I think?). I'll yell at @cola_colin to make PA Stats display server mods so that if this happens again we can discover the culprit.
I still think it is just a regular game. Everyone starts on the ground of the largest planet, and players move to other planets later. I have seen the black commander in middle game, it is just like a normal commander which walks on the terrain. I have no idea when he can fly.