Like many Elizabeth or Sparky fans, I have been very upset/angry/annoyed at the character changes for Season Four of Stargate Atlantis.

This is why I have created a (hopefully) concrete theory about why and how this has happened.

Many of you will remember the episode The Real World from Season Three of Stargate Atlantis. In this episode, John heroically saves Elizabeth by holding her hand and therefore helping her to break through the nanites' control. 

My theory is this:
Even though Carson cleared John, telling him that he had not been infected by nanites after touching Elizabeth, John was still infected with the tiny machines. The nanites, however, took their time to activate, doing so just before the episode Sunday.
This means that Sunday and all episodes afterwards are just a figment of John Sheppard's imagination. Due to John's very large hero complex he imagines a world where the people he loves (Elizabeth) and cares for (Carson) are killed. Plus the nanites are evil anyway so they fabricate this fake world.

This theory explains the whole of Season Four and those later episodes in Season Three which we also dislike.

And now to finish with a new favourite saying of mine: It's all in John's head and Elizabeth isn't dead!

Thank you