A/N - Thanks to my wonderful beta, Danielle. Thank you for all your help!
The timeline of this story is altered mainly concerning Daenerys, but also with the length of Ned's imprisonment is a little longer that led to a slight altering of Jon and Theon's timelines. Daenerys has already left Qarth by the time Ned is arrested.
"I am Eddard Stark, Lord of Winterfell and Hand of the King, and I come before you to confess my treason in the sight of gods and men. I betrayed the faith of my king and the trust of my friend, Robert. I swore to defend and protect his children, yet before his blood was cold, I plotted to depose and murder his son and seize the throne for myself. Let the High Septon and Baelor the Beloved and the Seven bear witness to the truth of what I say: Joffrey Baratheon is the one true heir to the Iron Throne, and by the grace of all the gods, Lord of the Seven Kingdoms and Protector of the Realm."
The High Septon knelt before Joffrey and his mother. "As we sin, so do we suffer," he intoned, in a deep swelling voice much louder than Father's. "This man has confessed his crimes in the sight of gods and men, here in this holy place." Rainbows danced around his head as he lifted his hands in entreaty. "The gods are just, yet Blessed Baelor taught us that they are also merciful. What shall be done with this traitor, Your Grace?"
A thousand voices were screaming, but Arya never heard them. Prince Joffrey... no, King Joffrey stepped out from behind the shields of his Kingsguard. "My mother bids me to let Lord Stark take the black, and Lady Sansa has begged mercy for her father." He looked straight at Sansa then, and smiled. "Lord Stark, is this your wish as well? Do you wish to take the black and serve the Night's Watch until death with your brother and bastard son?"
The crowd continued to scream for her father's death and throw rocks at him. Arya watched her father for a moment before he swallowed roughly and nodded. "I do, Your Grace."
"For my lady and to maintain peace in the Seven Kingdoms, I will send you along with the man from the Night's Watch. I denounce you, and attaint you, and strip you of all rank and titles, and do sentence you to take the black. Your eldest son will inherit your lands as long as he ceases the war in the Riverlands, swears fealty to the crown, and goes back to Winterfell, where he will serve as Lord of Winterfell at my behest," Joffrey said.
Since her father's imprisonment, Arya had heard little tidbits about Robb and the Northmen at war with the Lannisters. Would Robb be willing to end the war? Joffrey had just stripped her father of all of his titles and lands. He'd forced him to confess to being a traitor when Arya knew her father could never have been a traitor.
Arya felt someone pulled her off the statue and she tried to fight. A firm arm picked her up and dragged her into an alleyway. She tried to draw Needle but the man gripped her wrists too tightly.
"Do you remember me?" the man said quietly. He was dressed all in black, his clothes tattered and worn, plus he smelled funny.
At first, she tried to struggle again until he said, "Look at me boy. Do you remember me? My name is Yoren and I know your uncle Benjen."
"I'm not a boy!" she retorted, studying the man. He did look familiar but she had seen so many people coming and going in King's Landing the last few weeks, she wasn't sure.
"You are a boy if you want to come with me. You're an orphan boy going to join the Night's Watch," the man said. Pulling out a knife he began to cut her hair short.
Arya struggled until she realized this man would be taking her father with him. "Are you going to take me to my father?"
"Orphans don't have fathers. I'm going to take you north along with a band of misfits and criminals to join the Night's Watch. Might be the former Hand of the King will be with us. But if a boy is smart and wants to get out of the city alive, he'll remember orphans have no fathers and no homes."
Feeling confused but hopeful, Arya nodded. At least she'd be with her father even if she had to pretend to be a boy.
A few days after his confession, a young maester, not Maester Pycelle, checked Ned's leg, replaced his cast, and gave him some dreamwine to take with him for the pain. The gaolers then put him back in shackles for his journey north. Ned was just happy to breathe the free air and see daylight again. As soon as the council had confirmation that Robb had ceased his march to the Riverlands, Ned was prepared for his departure. Robb had given up the fight quite easily, desperate to save his father, Ned supposed. Ned felt humiliated that he had lost all honor with his lies in Baelor's Sept and now his son must rescue him.
At least Sansa had been allowed to see him before he left. Tears filled her eyes as she ran and threw her arms around his neck. Sansa attempted to compose herself, always the lady, but Ned could only see the little girl he was leaving behind with these monsters. He didn't trust the Lannisters to treat her well, but he had no choice in the matter.
"Forgive me, Father. This is all my fault. I never should have gone to the queen, but I hoped she would persuade you to stay. I never thought she'd do this." Sansa sobbed and spoke so quietly, he could barely hear her. "I want to go home, but they won't let me now. I was such a fool to trust them."
"Hush now, sweet girl. We don't have much time and the wall have ears. There is nothing to forgive. This is not your fault. But you must listen to me. Do not speak ill of the Queen Regent or the King. Ever. The Red Keep is full of spies and traitors. All your words can and will be heard. Do what they tell you and you should stay safe," Ned whispered in her ear. "Don't trust anyone, Sansa."
"I won't. Will they let you see Mother? Or my brothers? I don't know where Arya is and no one will tell me," Sansa said, wiping the tears from her eyes.
"Arya escaped the city, I think. I'm sure your mother and brother will find her. I doubt I will be able to see them, but if I do, I will tell them you miss them. When everyone returns to Winterfell, you'll be able to send ravens, but remember they will be read, so watch what you say."
"Eddard Stark." A Lannister guard stood in the doorway. "Your escort to the Wall is here." Ned hadn't realized how used to being called "Lord" he'd become until everyone stopped saying it before his name.
"I'm sorry, Father, for how I acted about Lady and for being so angry with you. It wasn't your fault. I love you so much," Sansa said, clinging to his tunic. Ned's heart was in his throat. He was the father; it was his duty to protect his family and he had failed. Arya was lost to them, Sansa pleaded before court for his mercy, only to be held hostage, and Robb forced to go to war for him. And this could be the last time he saw Sansa.
"Sweet girl, no matter what, I will love you. There is nothing you could do that would not be forgiven." Ned ran his hand through her hair and kissed her forehead. "You're as beautiful as your mother. You'll make a wonderful queen and the people will love you."
"I don't want to be queen now or marry Joffrey. I just want to go home," she sobbed.
"You are a Stark of Winterfell, Sansa, and winter is coming. You must be strong and act with honor," he said firmly. "Hold true to who are you, whether you are queen or sister to the Lord of Winterfell."
"Robb is now Lord of Winterfell, not me, sweet one," he reminded her. She nodded quickly, straightening her back and standing tall, despite the tears in her eyes.
"I will make you and Mother proud, I promise," she answered. He kissed her goodbye as the guards led him away. Sansa watched him go with wide blue eyes, looking much older than her years. She was truly her mother's daughter. He prayed to the Old Gods to watch over her in this nest of snakes.
As he was walking out, he saw Lord Varys, dressed once again like a gaoler. The eunuch moved to walk beside him. "Lord Stark, you did well. Your daughter should be safer now."
"I'm not a lord anymore. I've lost all honor and have been labeled a traitor," Ned said quietly.
"Would you have preferred an honorable death? That would surely leave all of your children at risk in this war. As it is, the Baratheons are still going to battle for the throne. Your son was wise to bend the knee. For now."
Ned walked a few paces then looked at Varys. "For now? What do you mean?"
The eunuch said nothing, offering him a small smile and stepping away as a Lannister soldier came to take Eddard's arm, forcing him to move faster. Ned saw that Yoren, the black brother he'd met previously, awaited for him, along with all of the criminals he'd scavenged from the cells, a few boys barely old enough to take the black, and, much to his surprise, Robert's bastard son, Gendry. Gendry watched him curiously as they loaded Ned into caged wagon, his leg too injured for him to ride. As they slammed the door to his new prison, the boy that had been talking to Gendry turned around and Ned's heart nearly stopped when he saw his younger daughter's eyes staring back at him.