This is a pretty simple scenario: what if one of the passengers aboard United 93 had been a pilot, and had been able to land the plane safely after the passengers retook the plane, rather than simply crashing it into a field?
Scenario: after retaking the plane, the pilot-passenger gets on the radio and calls whoever, identifying themselves and saying "We have retaken United 93. The plane is no longer under control of the hijackers. Requesting instructions."
Two scenarios come to mind. One is that, in the chaos of the FAA grounding all planes, United 93 simply lands at the nearest airport. More likely, the plane is guided into an airbase by jets. There's a very low possibility that it's simply shot down, but I doubt it - even on that day, someone would have to be awfully trigger-happy to shoot down a plane that's actively communicating.
I doubt the course of events vis-a-vis invading Afghanistan would have changed much, but the horror of 9/11 would have been blunted. The passengers would have been lauded as heroes, becoming celebrities overnight (and probably all receiving the Presidential Medal of Freedom), and writing numerous books about their experiences. If they'd somehow managed to take one of the terrorists alive, the resulting trial would have been a major cathartic moment for the US, and almost certainly resulted in a death penalty. The eventual United 93 film would have been an even bigger affair. I could even see one or more of the passengers trying to go into politics.