Desmond Died by Scott Gingold

It had been bothering me ever since the finale that because the flash sideways was revealed to be an afterlife, it brought in question the nature of Desmond's consciousness-traveling in "Happily Ever After" when Charles exposed him to the electromagetic energy in that chamber. Desmond was exposed to the EM and was "transported" to the flash sideways. When it happens he seems to have memories from the island (which is not that surprising since everyone in the flash sideways had some memories of their life on the island), but then when his consciousness returns to his island body, he has memories of his time in the flash sideways.

This fact has remained curious to me ever since, because it bears more serious implications. At first we're meant to think that Desmond had a similar experience to when he was time-shifting in the helicopter when passing through the island's time barrier in "The Constant." Now in "The Constant" I still believe he was time traveling, but this leads us to also recall his other main instance of consciousness-shifting in "Flashes Before Your Eyes" and that instance is the kicker. I think when Desmond turned the fail-safe key, he died. The flash we saw in "Flashes Before Your Eyes" when Desmond woke up in his flat with Penny covered in red paint was the flash sideways timeline. It explains the strange appearance of Charlie. It also explains why he remembers things differently such as the details of the football game and why he hears the beeping of the hatch in the microwave. And it really explains the words and actions of Eloise Hawking who seemed very similar to her flash sideways counterpart in that episode. What seals the deal for me on this theory are Desmond's words as he wakes up back on the island after being hit on the head by the cricket bat: "Please, let me go back. Let me go back one more time. I'll do it right. I'll do it right this time. I'm sorry, Penny. I'll change it. I'll change it." At the time I thought it meant that he would go back in time to do it over right again, but really what it meant was that he got a second chance at life again. His flash with Penny was his death and being hit on the head with the bat in his afterlife sent him back to to life to give it one more try.

A sidenote:
I know this is a lot to tackle in one theory, but the revelation of Desmond having died when he turned the fail safe key and then coming back to his island body, slightly different, with premonitions or should I say special, makes me think of the so-called sickness. Claire and Sayid were supposedly "sick." What both Claire & Sayid have in common though is that they both had near-death experiences. Claire's house was hit by the mercenary's explosive. When Sawyer picked her up the first thing out of her mouth was "Charlie" leading me to believe that she had crossed over to the afterlife (flash sideways) and saw Charlie before coming back to her island body. Sayid was drowned by the Others in the pool and according to Miles was dead for 2 hours before "coming back to life". Just like Desmond, when Sayid & Claire returned to their island bodies after dying, they were slightly different. While Desmond had premonitions, Sayid slowly started to lose all emotion, and Claire started to lose her sense of self/sanity. It was different for all three of them, but all three of them did have a near-death experience.