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Ned raised her along side his children, claiming her to be his own, it was the only way he'd been able to protect her. To keep her hidden from those who would either use her or kill her.
As she grew, blossoming from child to young woman, so many people said they could see Lyanna in her. They said she was the very image of his sister. That they could easily think her to be Lyanna's twin instead of her niece.
But Ned knew that was just because they did not know who Joana really was.
For all her physical resemblance to Lyanna, Joana bore none of Lyanna's wilful personality, none of her fierce temper or the ice that had made Lyanna who she was. Joana was, surprisingly, docile and quiet. She held honour and justice highly but believed both should be dealt out fairly and wisely. She was her father's daughter in more ways than she would ever know.
But she was not his.
Not truly.
He had claimed her, called her daughter and loved her as fiercely as a father should, but she was no more his than she would ever be Catelyn's.
There were times when he would look at Joana and see what other's saw. He would see Lyanna and it gave him hope, hope that he could forever keep her hidden. Keep the truth locked away in his memories and forget what he knew.
But there were other times when he would look at her and see a grace, compassion and a strength that Lyanna had not possessed. He saw a girl who, with the proper guidance, could become a strong and just leader. He saw what no one else saw because they did not know the truth. He saw a girl born of ice and fire. A girl born of two of the greatest Houses in Westeros' history. A girl who, had the Gods been kinder, would have been Queen.
He saw the daughter of Rhaegar Targaryen.
He saw the daughter of the Last Dragon, Princess of Dragonstone and rightful Heir to the Iron Throne.
He saw a girl who would be killed if Robert ever learned the truth.
Her being Lyanna's daughter would not matter. All Robert would see would be Rhaegar's child, a Targaryen child, a threat to Robert's rule.
So, to protect his sister's daughter, to keep his promise, he lied and kept the truth hidden.
He raised the rightful ruler of Westeros as his bastard daughter and watched as, every day, she grew more and more like her true father. And every day he prayed for her safety. Even when he knelt on the steps of the Sept of Baelor, facing his own death, he prayed that Joana was kept safe in the madness that was surely to follow. In his mind's eye he could see her face, see Lyanna's face with Rhaegar's stoic expression.
And as the sword swung he prayed that his sister forgave him for his failures when it came to her daughter.