The new season is nearly here, and I am getting very excited.
A couple of theories I have about the way things will turn out:
1) Helena left her liquid nitrogen canister with the fertilized eggs behind when she was kidnapped, and this will prove to be key to saving Cosima. However, the sisters are going to be in a bit of a dilemma, since "My biology, my choice" will come into play. The eggs belong to Helena, and she should consent to their use. I can see this being a source of conflict between Delphine and Cosima, as Delphine will want to use any means neccesary to save Cosima.
2) I think that, untimately when the fertilized eggs are analysized they will discover that Hank was not the sperm donor used to fertilize Helena's eggs. I think Hank knew that Mark was Project Castor and saw it as his duty to combine the two clone lines. This could work even if Mark was a double agent with the Proletheans, as he probably would see combining the clone lines as a way to further the project.
3) One thing I wonder about is that meeting between Paul and Mark at the bar. Their interaction suggested that Paul didn't know about Project Castor, but then later we saw Paul, with a bunch of the Project Castor clones. Did he just learn about Project Castor, or did he know all along, and just somehow knew that Mark wasn't a Project Castor clone that he had met before?
Oh, and something else that has just occurred to me:
4) If Mark is a double agent for Project Castor and not a runaway from the project, poor Gracie will probably find herself locked up with Helena again real soon. Whether the sperm donor for Helena's eggs was Mark or Hank, Project Castor is going to want the baby inside her.