A plot one of the stages of which included potentially crashing an airplane into WTC[0], among other targets, was uncovered (mostly, it appears, by accident) and thwarted in the mid-nineties. The Lone Gunmen plot coincidence is less curious considering that plot could have served as an inspiration, although the means of hijacking were very different in the series.

The sad thing is that uncovering that plot didn’t help prevent the actual attack based on it a few years later…

[0] https://en.wikipedia.org/wiki/Bojinka_plot#Phase_III:_CIA_pl...