I have an idea so we can continue with S1. We could treat the two parter as an unfinished story, or a missing episode and somebody else could complete it using information from Time Guardian's plot and Meet the Guardians. Here is a basic plot I came up with.
Plot: The Forgotten have reunited the two groups so it's easier to kill them all. The Doctor once again leaves Jenny as he and Morbius escape, but leave the others behind. This is because the humans have no power to make a time machine, but the timelords do, so the humans should be safe. The Forgotten begin chasing the Doctor, but he has a better time machine. Both of the time machines land on Earth, but the Forgotten turn back on Jenny who they plan to use to destroy the timelords. On Earth, the Doctor and Morbius plan to extract natural time from the vortex, making it unnatural time. They succeed and are about to use this Timebreech, when they both begin to fade from time. Amy and Rory manage to get the Forgotten off Jenny. The Doctor manages to seal the Forgotten back into time, and also fix time, but some of the timebreech still exists. Jenny realises she can't stay with the Doctor beause she'll always be worried he'll leave her. The End