My Theory

Jack, Charlie, Bernard and Cindy Chandler work for DHARMA Initiative along with a few others.

The plane never crashed on the island. Bernard placed a small bomb in the rear toilets and as he flushed it into the air it exploded creating a small confusion amongst the passengers. Charlie placed a second small explosion in the aircrafts toilet near the front which caused the aircraft to descend fast and the oxygen masks came down and all passengers were out cold. The oxygen masks did not provide oxygen, but a knock out gas. Jack was ok because he drunk a small bottle of medicine to prevent him form being unconscious, given to him by Cindy. Charlie was ok to as he took his medicine in the toilet, I can assume Bernard and Cindy done a similar thing.

A few moments latter Jack goes to the cotpit and then fly's the plane to a small island and lands it.

All survivors are part of a big experiment.

Bernard's reason for doing this was to cure his wife (rose) from cancer.

Jack reasons unknown at this time.

Charlie reasons unknown at this time.

Cindy reasons unknown at this time.

Jack and Charlie need to get to the cotpit with one of the main survivors because she came round when she should have been unconscious and may remember what really happened. So they set it up so Kate will go with them to the cotpit to retrieve the transceiver.   Charlie goes into what is believed to be the toilet to set off what we see as the monster killing the pilot, with all this Kate can't ask as she is in a group that all seem to fit together, latter Kate says she has seen Charlie before, Charlie response that he is a rock star from Driveshaft and a link is made, now Kate will forget what she remembers for now as her mind is satisfied.

I will add more soon