I think that's because The Last Ship already wrapped up its original premise of the global pandemic. It told a complete story. So at this point, if it is to continue past its original story, the show needs to come up with new global threats, related to the pandemic, in order to keep going. So, I can definitely see why season 5 will be the last. There is only so many new global threats that only the Nathan James can solve because the premise starts wearing thin. Similar to how 24 got ridiculous with Bauer always being the only one to stop the next big terrorist threat in 24 hours.
