If I had known I were going to successfully destroy the Rebel Flagship, I would have given my ship a better name!
[here is where I would post a picture of the victory screen if I were on my computer instead of my Kindle]
But default name or no, the good ship Shivan and her crew managed to pull off a harrowingly-tight victory against the juggernaut of a final boss that is the Rebel Flagship. The first form was easy--teleporting my guys directly into their weapon systems left them completely impotent. The second form was tougher: I had enough dodge and cloak to deal with the drone spam, but the boarding drones and their hull breaches took out one of my crew before I pulled it out. The final form was the hardest. Its uber-shield made it impossible to effectively damage. I had to send my boarding crew to sabotage the missiles, since they ignore my shields, but that left them unable to attack anything else. I timed my cloaking to dodge the surges but I couldn't dodge everything forever. They scored a hit to set my engine on fire and things started to spiral, but luckily by then my saboteurs had gotten to the shields and my lasers could tart tearing them up. Slowly. Slooowly Slooooooowly. While they were puking lasers and missiles at me.
But we did it! With our ship burning and our hull critically damaged, Shivan's crew fired the shot that destroyed the Flagship and made them the heroes of the Federation. I can only assume there was a medal ceremony with an epic soundtrack afterwards.