Historians absolutely do trace the spread of conspiracy theories, "the history of ideas" as you say. Sometimes there are obvious "patient zero" points (like the Phantom Time Hypothesis which was pretty much invented wholesale in 1991 by Heribert Illig), sometimes they spread organically (like the moon landings).

9/11 has so many conspiracy theories it's hard to comment on them in an all-encompassing way, but let me trace one I made sure to comment in the META thread the /u/Georgy_K_Zhukov linked -- that there was a missile that hit the pentagon. I'll just clip with that to start things off:

There is a conspiracy theory that the Pentagon was struck by a missile rather than a plane. This is absurd for numerous reasons, one being the hundreds who saw the plane as it approached the Pentagon (some observers even recognized the plane’s livery as belonging to American Airlines.) Second, nearly all the passengers from the flight were later identified by DNA testing. Third, one of the first responders, a structural engineer, said

I saw the marks of the plane wing on the face of the stone on one side of the building. I picked up parts of the plane with the airline markings on them. I held in my hand the tail section of the plane, and I stood on a pile of debris that we later discovered contained the black box.… I held parts of uniforms from crew members in my hands, including body parts. Okay?

We actually know where the story came from -- a comment from an eyewitness was taken out of context. Mike Walter, speaking to CNN:

I looked out my window and saw this plane, this jet, an American Airlines jet, coming. And I thought, ‘This doesn’t add up. It’s really low.’ And I saw it. I mean, it was like a cruise missile with wings. It went right there and slammed right into the Pentagon.

Note that the witness very clearly says they saw a plane, and later make an analogy to it being like a missile. However, if the latter part gets clipped without the first, it seems like the witness saw a missile.

The missile story became famous due to Theirry Meyssan and his 2002 book L’Effroyable Imposture ("The Horrifying Fraud"), which was a best-seller in France (despite being denounced in the media) and has been translated in many languages, published in the United States in English as 9/11: The Big Lie. Even though conspiracy theorists don't take all his claims wholesale, they are still the origin of some of them. 9/11 has so many conspiracy theories that many of them are mutually exclusive, so conspiracists need to pick and choose which ones they believe are true.

A good starting point collection for the most famous conspiracy theories (including counters) is Debunking 9/11 myths: Why conspiracy theories can't stand up to the facts by Dunbar and Reagan.

More can always be said, but /u/jbdyer and /u/tlumacz wrote an excellent overview of 9/11 for the sub here which touches on some conspiracism around 9/11, so would be a useful starting point for you.