Edited 10/27/13 for formatting tweak.
Phineas, Ferb, and the gang had managed to spend the day inside for once due to a summer storm. By the end of the day, Phineas and Isabella were left spending time together as everyone else discreetly went away.
Suddenly, the storm grew slightly more intense, and Isabella realized that she had to get home quickly; the Fireside girls were meeting at her place for a sleepover, and she hadn't prepared much.
She had barely finished telling Phineas about the dilemma when she saw Phineas scratching his head. "What's the best way to get you home..." he mumbled, until he realized:
A tunnel to Isabella's place could work for three reasons:
1.) He had already filled out and gotten approved paperwork for a tunnel anyway.
2.) It would keep Isabella dry and get her home quicky.
3.) It could be kept secret.
Suddenly, he knew what he was going to do tonight.
"I got it!"
Isabella jumped as he did.
"Be right back," he said, and ran off.
Off she went to Phineasland.
This time, she and Phineas were under an umbrella, his hand on her shoulder, hearts everywhere and-
"Hey Isabella, come with me!" he said quite suddenly, and took her hand.
And she ran with him until she realized they were going to his basement. A new door there, above which was a sign that said: "To Isabella's House", opened to a roomy, well-lit, but drab tunnel.
"I'm sorry it's drab but I know you have to get home in a hurry and-"
Isabella had stopped listening a while before; her dreams would have to be deferred for yet another day.
Phineas snuck back down to the tunnel that night; he couldn't sleep.
He sat down outside his door and wondered what could justify the tunnel's existence. A list came to mind:
1.) He had already filled out and gotten approved paperwork for the tunnel; it had legal justification.
2.) It did keep Isabella dry.
3.) It is his and Isabella's secret.
That's when he realized that he and Isabella don't share many secrets.
It felt weird to him because Isabella became very close to him, especially since the summer began. That, and they shared so many moments together. He spent much time basking in those memories until he recalled one secret he didn't share with anyone:
He knew Isabella liked him.
He confirmed this when one day, she and the Fireside girls came by to ask for help, and when he offered it, she began to daydream. Phineas, curious, asked Gretchen what Isabella could be daydreaming about.
She raised an eyebrow. "You never knew?"
That's when he realized that he couldn't say he knew.
But now he had the tunnel.
Maybe, he realized, he could tell her now.
Isabella also went down to the tunnel that night. Like Phineas, she too couldn't sleep.
Normally, whatever Phineas and Ferb did would disappear. This didn't.
She began to wonder if Phineas would ever go back to the tunnel. She hoped he'd knock, and she'd open the door, and he'd whisk her off into Phineasland, like he never did.
Then the door knocked. On the other side was Phineas, his hand extended.
And off she went.