Sam was getting frustrated at the useless books he was reading. Jack was going to die. Again. Dean happily taking their son to their death. Castiel didn't agree, neither did Sam. Dean. He went insane with grief. The grief of being God's puppet. Sam decided to leave. But not before talking to Cas and Jack.
He knocked on Jack's door.
"Come in." Jack says in his innocent childlike voice. Sam nearly teared up. That was his son.
"Jack. I need to tell you something."
Jack looked up from his laptop. When Sam looked at it, he was watching fathers and their children. One was ecstatic his child was going to college and was hugging him, telling him he was proud. Another was teaching his daughter how to play catch. Sam felt sad about what Jack was watching. He and Cas tried to do things with their son, but Jack clearly idolized Dean and was trying to make him happy. Sam hated Dean for abandoning their son. He had to take Jack away. To protect him.
"Jack. Pack your things."
"Why?"
"You and Cas are going on a trip. Pack light. Only the bare essentials. No laptop, no phone. I can't have Dean tracking you down."
"Is it because of God?"
"Yes. Jack. I love you as my own. A father is always supposed to protect his child. I don't want to lose you again. Jack, get ready."
"Okay."
As Jack packed, Sam went and talked to Castiel. Castiel teared up and thanked Sam for protecting Jack.
"Thank you Sam. What about you?"
"I have plans. Go. No electronics. Ditch the vehicle. Get a boring car, get new IDs don't go on any social medias."
"Okay. Will you and Dean be okay?"
"Yes. Now hurry. Dean may be back any minute."
As Cas waited for Jack, Sam quickly packed up whatever he could. He left behind everything. Except his SD card. Pictures of his family, Mom, Dad, Dean, Bobby and everyone he ever cared about. Once Jack was done, all three quickly left taking one the cars in the bunker, a classic convertible.
The last scene was them driving away into the night. Never to return.
Dean came back to the bunker expecting to see Sam, Cas and Jack doing research or yapping about their day. Seeing the bunker empty, he figured they went for a drive. A few hours later, was throwing a chair. Sam. He figured it out.
Sam waved goodbye at Jack and Cas. They had facial disguises and new fake IDs they paid cash for. They were heading to Iceland. It was far away from Dean and with Cas being fluent in every language on Earth, he knew they'll be okay. He teared up seeing the plane leaving. He was waiting for his own flight, but not on a plane. He was waiting for Michael. Michael and him were going on their own vacation.