If you're still wondering why the future that Phineas and Ferb went to in the show was so much different than the future they now faced with the nuclear war, it was because Titor traveled back in time and, pretty much, changed the course of their history. This can get a little confusing. As Titor said, going FORWARD in time is easy, as it doesn't change anything in the worldline you're currently in (the future hasn't happened yet). Going back in time, however, is impossible since it already happened, and so quantum physics has to make up a scenario where going back in time is even possible – that is called the string theory, which has an infinite number of worldlines.
Remember the conversation that Titor had with Kevin Flynn – that he had to step into the worldline directly next to his, so that it would be as much like his worldline as possible.
If you didn't like the ending, that's alright. It is only fanfiction after all, and can't change the course of the real show. You can also take into consideration that he show is a different worldline than this story. Either way, I just hope you enjoyed the story.
Special thanks goes to Larry Haber (the attorney for the real John Titor), Oliver Williams (who runs the biggest website dedicated to John Titor), George Noory (host of late night radio show Coast to Coast AM which was the show Phineas stayed up to listen to), Art Bell (former host of Coast to Coast AM), and Anonymous who wrote the excellent book 'Convictions of a Time Traveller', now available from Amazon.
Please take a look at some of my other fanfic, and stay tuned for more. See you in the future.
-H. H.