To the OP, I sent this to someone in a pm, not 100% mine some of it is from Bastard of Summer
I propose that Aegon is really the son of Rhaegar, as Varys says he is.
Now I choose to believe that Aegon is who Varys says he is simply because I think it can go both ways. Varys could be lying about his identity (He really could be the son of a Blackfyre), and Varys could actually be telling the whole truth this time.
Varys doesn't lie to people some members say. Well I believe that a half-truth is a whole lie (but that's neither here nor there) so for the purpose for this,I will stick to the boards majority belief that he does not lie. But rather he tells them half of the truth.
During Roberts Rebellion the Lannisters didn't join in on the war effort on either side until it was pretty much decided that Robert had won by killing Rhaegar on the Trident. So I propose that while Tywin and his two children were waiting for that news, so that he could declare his loyalty to Robert he had a message sent to Pycelle (who was in KL with Aerys and Jaime). The letter consisted of Tywins plans to join Roberts effort by sacking KL for him as a show of loyalty. Varys of course found this out. I believe this happened three ways with the same result.
1. the message was sent via raven. however one of Varys little birds (they are everywhere) intercepted the message to read it first (put the message back on the bird_ and got back to Varys with the info.
2. the message was sent by Tywin via a child (who was one of Varys little birds, but unknown to Tywin). Tywin thinking the child couldn't read didn't think twice about it.
3. On of Varys little birds just plain old over heard the plot while at Casterly Rock and got the message back to Varys as soon as it was heard. Or as soon as the message arrived in KL to Pycelle one of Varys' little birds got into Pycelle's chambers to read the incoming message as they would do all messages so that Varys could have the into. He's not called the Spider for nothing.
Now it take some time to get from Casterly Rock to KL, so before Tywins army could start to march the message had to go out. The message was sure to arrive before Tywin and co, because one bird or child could arrive faster than a host of hundreds or thousands.
So I propose that while Tywin was marching towards KL both Pycelle and Varys have the info of his impending arrival. Varys acts faster and he alerts Elia of the plot to kill her and her children (Yes it was premeditated. Tywin nurses a grudge like a good scotch. Remember his proposal to marry his daughter to the Mad Kings son? And the following rejection).
So this is where it gets all cracked and potted. Varys uses his secret passage know-how to get to and from Elia and children. He proposed to her that he can save only one of her children, just in case the inevitable demise via Tywins henchmen does take place. There is precedent for this taking place. Remember in the PatQ when Strong helps Aegon II and his remaining children escape from Rhaenrya when she arrives in KL to kill them? Unlike Strong though, he can't help them all escape because people would suspect it was him to help them escape, and he wasn't leaving with the like Strong did. So he tells her there is a woman in Fleabottom with a baby that looks just like new born Aegon. It could have been a simple switch, but if baby Aegon was born with a head full of Targaryen blonde hair, then it's not so simple. But he did find a baby with the same hair and she was willing to sell him the baby. If she's poor then child might have died of hunger or some disease anyway. So she took the gold.
Why would Elia agree to saving one and not the other? Well again there is precedent for this, again PatQ. When Helaena was forced by Blood and Cheese to choose between which child should live and which should die. She chose the youngest, but they killed the oldest anyway.
Elia might have chose to stay (just like Halaena did) and asked Varys to save both the children, but Varys told her it was his way or no way. I don't believe that she would be stupid enough not to try and save at least one of her children. So she chose the one that could be easily swapped and was virtually unrecognizable.
Sacrificing herself and her daughter to save the son. Who could one day avenge his mother, father, and sister
All the while Pycelle tells Aerys to open the gates. Varys after dealing with Elia goes to Aerys and tells him not to. Varys considers Varys info a lil bit, Aerys sides with Pycelle anyway. Tywins army goes on killing spree. Aerys feels duped. Tells Jaime to bring him Tywins head.....you know the rest of the story.........
Marwyn will take Aemons face a la faceless men, he will go to Dany and pretend to be Aemon. He will get close to her and kill one of her dragons or steal one. Is one of the people Quaithe warned her not to trust.