So I got my ark killed and I noticed something odd...
The game didn't end, the music just cut out and the AI thought I was dead. I could still control my ships and build things and metal income continued (I couldn't capture planets though). Without the ark the game would be very difficult, but it is odd that there was no game over screen or anything.
Also, on gaining vision to the whole map, I noticed that while there was two Mk V planets, there is only one master controller in the galaxy. This might be though because there is currently only one AI player.
Either way I'll put both of these on Mantis