Cryptic have stated that some of these missing missions will be remastered and returned at some point, although as time passes, this becomes less likely. This is because several missions have been removed from the game and several story arcs have been consolidated. One of which is that the central storylines are now somewhat confused. However, these changes have not been without consequence.
Cryptic have done much over the years to revise the game and make it a more linear experience. Over the course of its eleven year lifespan, Star Trek Online has evolved from a rushed, incomplete MMO to a far more coherent product.