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?