Comrade, I'm not saying this to dunk on you but when you reach these kinds of questions

is there proof that the plane actually left and is a real passenger plane that was scheduled?

you're delving into QAnon/Flat Earther-type thinking. Once you start with conspiracy first, explanations later, you're dangerously close to going off the deep end.

If all these very reasonable responses don't convince you that the US didn't bomb themselves with a missile, then I'd urge you to ask yourself if there is anything that would convince you. What would be enough proof for you to go "Ah, oh well, I guess it really was a plane that crashed into the pentagon"?

Because you can literally always say that evidence was faked by them but, well, then you've successfully made your theory unfalsifiable and have officially reached QAnon territory. I'm sorry if this sounds patronizing but I genuinely find this concerning.