I have scoured every second of this episode for hours and this is my solution in 10 easy steps.
1. Sherlock asks his friend Molly to provide a body that looks slightly like Sherlock from a distance, hence the phrase "I need you." His brother Mycroft has hired out the street with government actors. He then plants the false story of Mrs. Hudsons shooting to get John out of the way, if he thought she had been shot, he would have gone in an instant, as he threw a man out of the window repeatedly for giving her a minor cut.
2. Molly drops the body from the first floor window onto the ground, John doesn't notice because he's staring at Sherlock.
3. Sherlock jumps from the building, into the bin.
4. John mistakes the body for Sherlock's, and begins to run towards it
5. The cyclist, (probably a member of Sherlock's homeless network mentioned earlier in the episode) knocks John over, rendering him unconscious for a few seconds.
6. While John is down, the crowd of actors gather, and Sherlock swaps places with the body, the rubbish truck is then driven away by one of Sherlock's most trusted friends (possibly Irene Adler (The Woman))
7. The crowd put fake blood on Sherlock.
8. John begins to run again.
9. Sherlock takes out the squash ball (which he has been seen bouncing against the wall earlier on in the episode) and squeezes it under his armpit, temporarily blocking the pulse in his arm.
10. John can't find Sherlock's pulse, and the 'dead' body is taken away by the paramedics. Molly calls in a few favours at the morgue and Sherlock is officially announced dead.
This explains why Mycroft is so unemotional at Sherlock's death, and is glancing through the paper to check that his idea worked.
And there you have it, my theory in full.
And remember, after the impossible has been disproved, whatever remains, however improbable, must be the truth.
Elementary, my dear. My brain.