Originally Posted by FriendlyFacez

How exactly does the whaleship work, anyway? If I send forty characters out on the whaleship, are the characters on my four 'regular' teams unavailable to join in?

As fghk0 noted, the crew/squad rosters are separate; you can assemble whaleship crews with all of your normal mission squad members. Whaleship is essentially just another type of mission; you actively run each map as you would any other kind of mission. The only difference is that mob levels are higher, and there's a mechanic that uses the aggregate TP of all 8 squads to power the whaleship itself (which acts as simply one single unit- the whaleship maps are entirely single lane) in order to attack a super-boss pest (the Ancient Pest).