It would be an understatement to say that Phineas and his friends were not adjusting well to the aftermath of the whole situation. Even Vanessa, the dark goth woman that she was, admitted that she was not adjusting well to her new life. She had sold all her things and moved back in with her dad. She didn't go to see her husband, or ex-husband as soon as the divorce papers were finalized, in prison. Though no one was allowed to see him anyway. He was deemed too dangerous for anyone to see. Phineas even had to make a special cell for him to live in to make sure he never got out. That was hard enough for him to go through as it was. But now he had to deal with the fact that his brother had betrayed him.
But just like any story, there is a silver lining. Candace and Jeremy Johnson welcomed two baby boys into their family, Xavier and Fred. Little Amanda was overjoyed to have two younger brothers to take care of and it took some of the pain off the family. Losing Ferb like that was hard on everyone, especially Phineas and Isabella.
At first, Phineas was too afraid to marry Isabella. This entire thing started with him proposing to his girlfriend. If they had just stayed friends, his brother would still be with him and everything would be normal. However, after much prodding from his sister, he finally agreed to marry Isabella. Instead of the big wedding they were hoping for, they decided to just get married at the court house, with Jeremy and Candace as witnesses. Isabella was glad for this. After being kidnapped by her best friend, she realized that being married to the love of her life was more important than some fancy ceremony. They did have a little reception for their friends and family, but it was not grand or over-the-top. In fact, there were no Big Ideas anywhere to be seen. All of the old blueprints were burned. Even some of the inventions were destroyed as well. It was as if the Flynn-Fletcher dynamic duo never existed.
"Here, I brought you some cake," Phineas said, pushing the piece of cake with his foot through the bars. He pressed a button on the wall that made sure anyone touching the bars got an electric shock that would knock the socks right off their feet.
"You're going to have to say something soon," Phineas said after Ferb had said nothing.
"Isabella and I are married," Phineas said, rubbing the back of his head. "I know you don't care but I still believe that somewhere, deep down inside, my brother is still there. The one I made impossible inventions with over the summer. The one I told all my secrets too. The one I loved so much.
"We're also expecting a baby soon," Phineas said. "Isabella says it's a girl but I think it's going to be a boy. One of us has to be right, right?" Ferb still stayed silent and Phineas sighed.
"I wish you would have told me," Phineas said. "A girl never should have gotten between us, even a girl like Isabella. She was our friend but we were brothers. We should have been able to get through this." Phineas sighed again and turned around so that he was no longer facing his brother.
"I don't know what else to say," Phineas said. "So goodbye." With that, he left the room where his brother was being kept, never to hear his voice again, never to have his normal life again.