Danny loved her, like a sister, a daughter or something in between, but Ellie was happy as long as he was there to take care of her. She felt protected but couldn't stay forever.
She had already explored the whole world, and as interesting as the Infinite Realms seemed in reality they didn't interest her that much. Ellie was sure she needed to go further, but she didn't know how to let Danny know. So she simply told him straight out, that the universe they were in was no longer enough for her.
Danny accepted it, and told her that there were many other universes that she could explore, he told her that Clockwork had told him about some of them. Ellie was excited, she could travel more, but for the first time she hesitated, and realized that she didn't want to travel alone.
She asked Danny if he wanted to travel with her and he gave her the flattest look in existence.
"Obviously I'm going to travel with you" he said. And that was that. No discussion, no questions asked.
They both packed a couple of backpacks as if they were going hiking and asked Clockwork. He just tossed them Dan's thermos before offering them a method of travel. Danny frowned but opened the thermos anyway and dragged Dan with them as he yelled about injustices and upset families.
They ended up in Gotham, in front of a man with a helmet and a guy dressed as a stoplight. Danny waved and asked them for a chat (he probably wanted to ask for directions) while Dan sulked in the back. Ellie looked at the architecture curiously.
Unfortunately for Danny, the stoplight guy pulled out a sword and the helmet guy pulled out a gun. They both looked tense as they looked between the three of them. Danny frowned (his green eyes glinting with annoyance) before nodding towards Ellie and Dan and disappearing.
Thus began their vacation in a world where everyone wanted to shoot them; Danny felt at home, Dan wanted to steal an exotic candy called crypto-something and Ellie was happy to explore.
Their family trip had officially begun.