Gendry is Cersei Lannister and Robert Baratheon’s son.
Hear me out.
When Cersei goes to visit Catelyn in S01E02, (The Kingsroad), she tells her about her firstborn son.
“I lost my first boy; a little black-haired beauty.He was a fighter, too. Tried to beat the fever that took him. Forgive me, that’s the last thing you need to hear right now. It was years ago; Robert was crazed, beat his hands bloody on the wall - all the things men do to show you how much they care. The boy looked just like him.Such a little thing; a bird without feathers. They came to take his body away, and Robert held me. I screamed and I battled, but he held me. That little bundle; they took him away and I never saw him again. Never visited the crypt, never…“
Then, in S01E04, (Cripples Bastards and Broken Things), Eddard Stark finds himself retracing the final steps of Lord Aaron. That journey takes him to a blacksmith where he is introduced to Gendry. In stark (possibly deliberate) contrast to the physical image painted by Cersei, the blacksmith describes Gendry by saying he is “strong for his age.”
Gendry explains that Aaron had asked him about his work, and then about his mother. When prompted by Stark to tell him about his mother, Gendry says:
“She died when I was little; she had yellow hair, she’d sing to me sometimes.”
Ned then, after examining his features, put it together that he was the bastard son of (King) Robert Baratheon.
My theory is that something prompted someone to remove Gendry from his home and raise him outside of his family. Maybe because they were afraid of another rebellion and thought keeping the heir out of people’s knowledge was the best way to preserve an heir, or perhaps a witch or someone else who could see the future foresaw the War of the Five Kings, Robert’s death, Joffrey’s reign, etc, and saw it a necessity to keep him out of harms way until his time came.
The fact that Cersei never saw her son’s body after he was taken from her - never went to a wake, a funeral, or the crypt - means there is no tangible proof (at least in the story as it’s been presented) that he actually died! He was taken from her at a young age, and was told his mother with yellow hair died when he was a young child - the timelines (apparently) coincide - he is definitely old enough to have been born before Joffrey, with years in between for him to have been “little” when he was taken.
There are few ways they could prove it; it’s not like they have DNA tests. One possibility (and my favorite, by far) is Cersei actually seeing him and knowing in an instant that he is her son. You could also have a number of mystical destinies and components come into play, if he was taken from his family because of some sort of prophecy (as we found out last season, Cersei was foretold a prophecy about the fate of her children and it has unfolded 2/3.)
Going off of that prophecy, actually - the prophecy foretold three children all with golden hair and golden shrouds. Had Gendry/her son actually died, would there not have been a fourth shroud? Assuming the 3rd is meant for her third golden-haired child.
Maybe the Red Woman saw his prophecy - maybe that is the reason he was so easy to find when she needed “King’s blood”. She knew who to look for.
I’ve had a few theories since binging the show (haha) and this is by far one of my favorites (and definitely the one that holds the most credence thus far. I’m watching it all again to see what else (other theories or support for this one) might come up.)
UPDATE! Sept 2, 2016
The prophecy about the golden hair/golden shrouds panned out when Tommen killed himself, which means the witch did not foretell the death of a/the fourth child…so he has to be out there somewhere.
What I can’t help but wonder is who would technically have a better claim to the throne at this point? A Baratheon or a Targaryen? Because if this plays out we would have Gendry who is a legitimate heir to the family currently sitting on the throne, Danaerys who is a legitimate Targaryen, and Jon who we know is a bastard but also the son of the oldest of the Targaryen children, so I’m not sure if it could be argued that he would precede Dany in a line of succession.