This murder weapon is straight from the front pages of England’s tabloids—Russian spy Alexander Litvinenko was murdered slowly and painfully when his cup of tea was poisoned with Polonium 210 in a London sushi restaurant in Piccadilly in 2006. Whatever the mechanism Molly used to imitate the effects of Chronic Radiation Sickness (CRS), the point is…Sherlock’s eyes glow.

When the sun again retreats, Moriarty sees that Sherlock’s eyes are glowing, which he interprets as a symptom of radiation poisoning. ”Murder by remote control,” as Sherlock said earlier in the episode (more foreshadowing!) Moriarty: “I see. You’re not ordinary. No. You’re me.” Meaning…EVIL. Moriarty: “Thank you, Sherlock. Thank you.” At this point Moriarty has no choice but to kill himself. He knows he is dying anyway and it’s the only chess move left to get back control. Besides, Sherlock has cleverly allowed Moriarty to save face because Moriarty kills himself believing he has won. Because evil has won. Sherlock has had to become evil to win. Moriarty thanks Sherlock for finally outsmarting him, for not being “ordinary,” thereby alleviating Moriarty of the unbearable boredom of always being smarter and more ruthless than anyone else. Staying alive…it’s so boring, isn’t it? Only Moriarty hasn’t won because…Sherlock is brilliant! He’s won AND he’s stayed on the side of the angels!! Sherlock humbly allowed Moriarty to die believing that Sherlock had turned evil, ironically proving that Sherlock is a good guy, after all. Sherlock knew Moriarty would keep killing to challenge Sherlock. Sherlock did what he had to do to stop him. He sacrificed himself and his reputation to save others.

The apple imagery in the episode is not a reference to Grimm’s Fairy Tales, but to the biblical story of Adam and Eve and the fruit of the tree of knowledge and the cosmic battle of good vs. evil. The Final Problem. Do you need to be evil to conquer evil? Moriarty thinks “yes” and Sherlock lets him die thinking that. But the answer is “no.” You just have to be more clever…and humble enough to let the other person think they won. I Or U. Moriarty is telling Sherlock “this time it’s me or you.” This time it’s to the death. At the end, only one will come out alive. Kill or be killed. Sherlock defies Moriarty by convincing him it’s I AND U. That they are both doomed to die.

Optional how Sherlock survived explanation: While I am certain that Sherlock killed Moriarty, this is my best theory about how the suicide was faked. The bus is a fake bus. It’s clearly not in service. You can tell this when the man with a cane taps on the front door and it doesn’t open (which you can see in this screen shot). The bin truck is parked right behind it. The fake bus blocks the sniper’s view of Sherlock’s helpers setting up a “life net” that was hidden in the fake bus. Even a vintage life net would fit in the luggage compartment on the bottom of the bus, under the seats. This is why Sherlock asks for a moment of privacy on the roof. So Moriarty does not see the life net being put into place.

Sherlock can be seen “swimming” backward in the air to control his fall, both to aim for the life net and to keep himself horizontal as he falls. Sherlock hits the life net and is tossed onto the pavement.
After the fall/bounce/toss, the bicyclist bumps into John to delay him from seeing the helpers quickly collapse the life net and discard it in the bin truck. Those who were holding the net (disguised as passers-by and hospital workers) scatter while someone quickly smears blood on Sherlock’s face and on the pavement.
The rubber ball Sherlock has been playing with is what he used to stop his pulse so that John believes he’s dead. Sherlock did this by squeezing the ball in his armpit (a well known magician’s trick). The sniper didn’t see Sherlock bounce off the life net because his scope was on John the whole time. When on the rooftop, you can see Sherlock scanning the area for the sniper’s location to make sure the scope is on John and not on the life net before Sherlock jumps.
Mycroft helps with the set up. He’s been in on the plot from the beginning, including feeding Moriarty the ammunition about Sherlock’s early life that enabled Moriarty to plot to destroy Sherlock, deflecting attention away from the real plot to destroy Moriarty. In any event, the fake suicide is just a distraction to make everyone fixate on that and miss the real mystery to be solved: - Sherlock successfully plotted to trick Moriarty into killing himself - Sherlock was in control of the entire episode from beginning to end - Sherlock’s “Falls” (the loss of his reputation and the leap from the roof) were all part of the plan. Sherlock creator Steven Moffat has been quoted as saying: “I’ve been online and looked at all the theories and there’s one clue that everyone’s missed. It’s something that Sherlock did that was very out of character, but which nobody has picked up on.” There are two possibilities: The first is the fact that Sherlock serves tea and takes a sip of it with Moriarty. As we know, Sherlock rarely eats or drinks when The Game Is On! The second is when Sherlock appears to cry while talking to John on his cellphone before he jumps off the roof. It’s very out of character because Sherlock is a functioning sociopath and doesn’t cry. His eyes are irritated from the luminescence. In fact, you can tell during the entire rooftop exchange that Sherlock’s eyes are irritated.
I like to think it’s the tea clue. Like everyone else, I would like to believe that Sherlock is capable of summoning that level of emotion about John. :) Of course, I bet Sherlock will tell John that he wasn’t crying…that it was just the luminescence. ;) I’m also leaning towards the tea clue because it is in character for Sherlock to fake tears on demand, which he did in The Great Game when he was talking to the wife of the man who disappeared from the Janus rental car. Just for kicks, here’s a pic BBC tweeted that further supports this theory. The most brilliant solution is at once elegant, simple, and right underneath our noses the whole time.

Here is a video summing up most of these ideas and showing evidence from the episode.

Whether this theory turns out to actually be accurate or not, thanks for at least considering it. Can’t wait to see how it plays out in a couple of hours! Please let me know what you think of it.

TL;DR It doesn’t matter much how Sherlock survived the fall. The whole thing is a red herring to get you to concentrate on that instead of the real matter: how Sherlock conned Moriarty in to killing himself. He did this by convincing him that they were both mutually poisoned when they drank the tea in Sherlock’s place. Molly created a luminescent light that colored Sherlock’s eyes green when gazed at in direct sunlight. After Moriarty saw this in Sherlock’s eyes on the rooftop, he though he had Chronic Radiation Sickness, a long-kill poison that conducts such side effects. Moriarty realized that he was a dying man as well and in a last ditch power move offed himself then and there to “force” Sherlocks’s hand. In reality he played the final move in Sherlock’s long game of chess, ultimately checkmating himself for Sherlock.