It never made sense to me, since the hangar map had the boss start from a spot well inside the ship while the normals appeared to be beaming in from elsewhere, so I assumed that was indication the ship was his, but at the same time, more than one boss ship seems like a pretty big thematic inconsistency. Regarding arrival at the courtyard, the story basically went that we got lost while partying in the anniversary nega-void or whatever and ended up here. A map rotation mechanic wouldn't really support anything other than the idea of it being one big game centered around one ship, unless we can contrive a better reason for everyone going around in circles over and over again.
Where the boss spawned in the hangar was an elevator shaft. The bottom was closed off and you could from the bosses spawn, look up and see a door farther into the ship up there. The idea was the bosses infiltrated the ship and the players were defending the hangar before the boss could lower the shields to let a boarding party on.
Map rotation could be showing the different battles of different ships. You said yourself right there the party got lost in the nega-void. The fleet slowly got broken up and the bosses attacked. The individual ships have been defending themselves since in each part. the reason it keeps going in circles is because the it shows all the different battles going on at once. That could also help settle the new maps being added, new battles just starting. This also explains if we added in orbital strikes since that means the ship is just defending others on the ground. Interior maps could be part of a same battle in a different location. We could go into the pattern of on ship off ship, going to next ship defending itself and then looping back around. So only two new mini-bosses to make if there are only two different basic kinds of setting.
Plot just developed for the server: One day a group of players were messing around in the bedroom. Than another group of players called bosses came in and tried to ruin there fun. The players decided to defend themselves against the bosses and try to make them go away. Right when the players were about to defeat the bosses once and for all Kompressor, lord of shadows. Sent a wave of dark-matter called "shaders" to destroy maps. The players had 6 months before the wave of darkness hit and they spent that time in community builds constructing large ships, Server Settlers (SS) to escape the maps and head off to find new servers to settle in. The bosses used that time to regroup in larger numbers and attack the players once more.
One day while traveling amongst the stars. The bosses attacked the fleet. The capital ship heading off to settle Pecon7s server (named SS Pecan for that of course) was infiltrated by the bosses and was about to be taken over. The players held out in starboard hangar-A had to defend the hangar long enough, so the bosses could not lower the shields to let a boarding party on from one of the bosses vessels to take over the ship; and then fleet. The players bested the bosses once again but learned something new. That the bedroom was lost in the negative-light void (nega-void), and that once a year there would be an opening where players could go in.
Trying to rescue all remaining players the capital ship branched off from the fleet with a planned regrouping later to go in and save everyone left in the bedroom. There were still some bosses there though leading to another conflict. The players won once again, good over evil, and then went off to regroup with the fleet. The players got lost in the void though and ended up at one of the bosses many bases. With the capital ship not returning the remaining ships went into a power struggle over who would take control of the fleet. With all the different ships having there own ideas of where to go they all got separated. The ever so patient bosses found this to be the perfect time to strike and attacked all the individual ships.
That leads us to today, the capital ship is currently still in battle with the bosses, and all the other ships alone and separated and are being attacked right now. The goal of the current group of players is to defeat the bosses and destroy the base.