With the introduction of the Marked this season, the show has developed more subplots than any show should have and they have left characters dangling. For example - Maia. She now has her own subplot about enjoying her parental re-creations, but why hasn't she been joined in the new main plot of the Marked vs. the Promicin crowd. The Marked have sort of been explained in that they don't want the future changed by the crowd that created the 4400. Thus they "created" Isabelle to wipe them out, but then the gov't stepped in and corralled her.
They have given the Marked such an involved plot that they should have their own show.
If the show ends this season, then Tom will recover as someone will travel to the future and destroy the Marked. Jordan will see the light about testing for compatibility and create a Utopia where "outsiders" are encouraged to visit in order to learn how to save the planet. Everyone will live happily ever after, or will they?
The whole show is just too convoluted right now to make much sense.