My first reaction when seeing the film was that the show jumped the shark -- wasn't impressed at all.
However one thing to note is that after rewatching the film portion a couple of times I'm pretty clear parts have been edited out -- some of the jumps in the narration can't be explained simply by bad audio masking a word or two -- so we may not actually know what we think we do.
As for the people holding Michael et al, my money is definately on them being the people from the tail section, and chances are they're paranoid either because they're sick or because they've has run-ins with the actual others.
Finally, don't forget to visit the
Hanso Foundation website to learn a little about the scientists from the film.