I posted this on BGG, but thought I might get a quicker, more accurate reponse here.
Ok so I was trying this out solo, playing two Strike force ships (Vigilance, Ranak Warbeast).
Let me see if I can describe what happened. The start of the game I placed the opp. ships 1-2-1 (Technovore). My forces attacked and destroyed the opp ship in the right sector. During Aftermath a mission card had an Aftermath event that brought out an opp. ship to the center (now totally 3). This now caused the sector to be overrun(we had to flip 3 station cards. My understanding is that since the ship came out during the aftermath event phase it is considered unengaged so we merit a station card flip (this i may have got wrong). This triggered the Technovore Flagship to enter play.
As the next round began a travel event in the sector with the flagship instructed me to move the ship with the most [E] to the sector with the fewest ships, so with 2 opp. ships in one sector and my two strike force ships in the either .. we chose to move the flagship into our sector.
Through some great cards I was able to install tech and use boosts to get Vigilance attack to sixteen .. more than enough to wipe out the Hive Master ...
we easily won on round 2 ... did I miss something?
The Hive Master would come out with 6 weaponry and 8 defense.
16 weaponry would deal 8 energy damage to it (16 - 8 = 8), which would reduce it to 6 weaponry and 0 defense. It would not be destroyed. Though you would most likely have won on the next turn.
"Damage Event: Each engaged Ship compares its [ W ] to its opponent’s [ D ]. If a Ship’s [ W ] exceeds its opponents [ D ], remove [ E ] equal to the difference."
Also just to make sure, since you got your ship powered up so quickly.. when you requisitioned cards, did you put them on the bottom of your deck, or in your hand?