Rebel Flagship respawns?

[CptConfused]

I was relieved to finally defeat the Rebel Flagship but as soon as the battle ended it had reappeared at the edge of the sector and I was due to fight it all over again.

I'm not sure if this was a bug or if it's supposed to happen but I took from the name The Last Stand that it was a final showdown, not successive battles against the same enemy with an ever shrinking number of missiles to do it with.

Can someone clear this up for me (with a spoiler warning if necessary) because it left me feeling disappointed after the initial buzz of beating the boss.

[Matthew]

COMPLETE SPOILER BELOW



The Flagship has multiple stages, so in a sense he must be defeated multiple times but he's different every time and gets smaller as he gets closer to death. How many times did you defeat him? After the first stage, it should show him jump away the the event text says something along the lines of "He somehow managed to jump away." (extreme paraphrasing)

[CptConfused]

Ah ok, I only beat him the one time but didn't see any event text so I assumed the whole encounter had somehow reset. I panicked thinking it would be the same ship and flew around the remaining repair nodes to try and replenish my missiles, he got too close during that time so I didn't see the 2nd stage. Eager to see the other stages now, ty for the quick response and explanation