I really like the concept, but would stress that the mystery of what is going on will be what really hooks the players.
I would suggest (and maybe this is part of the plan already) to have things in the current timeline not always as they appear, and having the flashbacks shed light on current events (a perceived good guy is really evil, remembering a secret that can help in the present, etc.).
Also, I would experiment with the reason why they were drugged. Perhaps the drug was taken as an antidote for a magical disease the party contracted. Give them clues early on, or multiple sources of a similar effect, to keep them guessing.
If you really wanted to get out there, perhaps the "current" timeline are really flashes of the future if they don't achieve certain goals in the present. Maybe the bad events in the present were actually caused by the PC's in the flashbacks. Or, perhaps while the flashbacks appear linear, they really aren't (think of the movie Premonition).
Finally, remember that your pacing will be critical, and if you've seen the tv series Lost, I'd channel it - for every answer there are two new questions to ponder. I would make sure every game session gives them answers, but at the same time poses new questions. At first, more questions then answers, but progressively making everything clearer. A session or two early on should have more answers than questions, just to help with the feeling that the story is going somewhere. Oh, and the best technique is to have a final reveal at the end of the session to keep the players wondering what's going to happen next. Not every session, but a cliffhanger for the next session will help ensure interest.
My $0.02