in the darkest nights

Soon after the burning of Lord Chelsted, King's Landing was informed of the death of Rhaegar at the hands of Lord Robert Baratheon during the Battle of the Trident. Aerys evacuated Queen Rhaella, who was as yet unaware of her pregnancy,Prince Viserys and the Princess Vaella to Dragonstone along with the Red Keep's master-at-arms, Ser Willem Darry.

before the kings death, he made sure to hide Elia and her children, potentially sending them to dorne where they remained protected and hidden. This is just a rumor.

With the death of King Aerys and the suspected death of Rhaegars family, Rhaella crowned Viserys kind of the seven kingdoms, although the great houses recognized Robert Baratheon as the new lord of the seven kingdoms.