He helped Amy get her stuff from the house that she wanted to take, not trusting to leave her alone with her "parents." Something was wrong with the whole situation, besides the fact it was the wrong universe. He sat on the bed and watched Amy pack clothes and a few personal belongings.
"Take everything you want," He advised her. "Once we leave this universe I am going to close the crack again and hopefully this time it will stay closed." He stood up to where she had pictures tacked around her mirror and looked at them. He noticed all of them were Amy with friends and one man in particular, who he assumed to be Rory. None of the pictures included her parents.
"I'm ready." She said finally.
"Don't you want these." He asked gesturing towards the pictures. She shook her head no.
"I have copies in a photo album I packed." He helped her place her stuff in the car and watched her climb in without saying goodbye to her parents.
"Amy, you are never going to see them again." He mentioned to her.
"Good." She replied. The trip over to Rory's house was quiet and she went alone inside and returned not even twenty minutes later with him. He tried to talk to them as they drove back to Pete's house but receiving no answer he instead rambled on about the differences he had seen so far between the two universes.
As they pulled up to the house, he saw Rose sitting on the front steps of the house with her knees pulled up to her chest and her head buried. Her body was shaking as she cried. He quickly got out of the car and ran over to hold her. He sat down and pulled her into his arms and she turned and held onto him crying.
"What's wrong?" He asked her knowing if it was something serious she would have called him, rather than waiting for them to return.
"Mum won't come back." She managed to tell him between sobs.
"I'm not surprised. They have a life here."
"That's what she said." Rose sobbed.
"Come on. Now that Amy is with us, we need to leave. I don't want to risk the Tardis any longer than we have to."
They said their goodbyes and grabbed the few things they had managed to accumulate in their short time in Pete's world. They stopped by Torchwood to pick up Martha and Mickey and he wasn't surprised when John offered to go to. The drive and then balloon ride back to Bad Wolf Bay was quiet.
"I'll miss you," Rose cried wrapping her dad in a hug. "I'm sorry we can't stay."
"Don't be sweetheart. The universe needs you." He replied kissing her head.
"I wish you would come with us."
"I know," He said and then bent down and hugged Kiam before turning to the Doctor. "Take good care of them for me."
"Always," he answered and unlocked the Tardis. Rose headed quickly on board not looking back and Kiam followed after her with Mickey and Martha.
"Please take me with you." John asked him again.
"This universe needs a Doctor too and the Tardis will be ready soon enough. I know how bad we are at being patient but you just need to wait a little longer."
"What if I were to travel with him?" Amy spoke up.
"Amy?"
"What if Rory and I kept an eye on him? You have Rose and Kiam, he is going to need someone too."
"No, absolutely not."
"I think he should," He heard Rose say and he turned to look at her shocked, not realizing she had come back out.
She walked over to her dad and handed him a photo album, "To remember us by." She told him before turning back to the Doctor. "You left him here to look after me and for me to make him a better person. Now he is alone here and there is no one to help him. You are no longer the last of the Time Lord's there are so many more who can help him now."
"Me and Koschei are the last Rose. River, Kiam, Jenny, Donna and even him are only echo's of what could have been." He told her sadly. He looked at John. "Where is your Tardis." He asked him.
"Here," John replied and pulled a backpack out of the truck.
"Get on board before I change my mind." He said and he watch John hug Pete before disappearing inside.
"The universe in your hands Amelia Pond," He said softly as she led Rory inside.
"Thank you," Rose kissed him on the cheek and then disappeared inside again leaving him alone on the beach with Pete.
"I am going to try to seal the crack's permanently this time, sealing this reality off forever."
"Before you go Doctor, you should know there was a man poking around Torchwood a few weeks back. He said he was looking for a lost piece of technology but refused to tell me what it was, when I asked him."
"I am sure you know how to handle it."
"We did, but he called himself Koschei." Pete said.
"I will figure out what he's up to." He told Pete and then nodded at him. He headed back onto the Tardis to see that John had all ready removed the minimum power settings. He put back the insignificant power source and left Pete's world for what he hoped was the final time.