The last episode should have involved a final showdown with Suspiria in which Kes returns, persuade Suspiria not to destroy the ship and explains the reasons why.
Suspiria gives her a human lifespan and she's ready for a new, exciting life in federation space.
I forgot all about Suspiria. If Voyager had not gone so hard with the Borg, bringing back Suspiria would have been pretty cool. It did seem like once the got to Borg Space (And bringing in Seven), everything that happened before that was pretty much left behind.