Though I think this is less of a conspiracy theory and more of an open secret.
I believe the DOD(now DOW) wanted to turn Starship into a defense contract after flight 4 of Starship - a flight that proved that tower catches were possible and that the upper stage could survive reentry - and all the FAA, EPA, and leftist media bullshit attacking SpaceX after the launch was all directed by the Pentagon to try to manipulate Elon Musk into giving the DOD oversight and control over his Starship project by making it look as though the DOD would be the only launch license provider available. BTW, if you want to know which journalist is sucking Pentagon dick, its
Lora Kolodny
Why?:
I don't think anyone knew that Starship would actually work. I think the Pentagon just assumed that Elon Musk was full of shit, trying to push an inevitable boondoggle, or was just intent on selling full-flow staged combustion methalox rocket engines and created a fake rocket system for that goal. When flight 4 happened, they realized he was actually serious and also that the rocket wasn't another flawed design like the N1 or OTRAG. The Pentagon's paranoia is Russian-tier when it comes to advanced technology(Hell, DARPA exists for a reason) and they panicked after that flight since they didn't want China or Russia knowing that America technically has the technological capability to deploy troops and supplies anywhere on earth in less than an hour. Without IFT5 proving the accuracy of the booster in a definitive way, foreign countries would never know it could succeed.
Underlying Cause:
A side effect of allowing commercial space flight is that companies can do R&D with a degree of secrecy. Since such projects aren't defense contracts, the Pentagon can't be allowed to have unlimited oversight since there's too many assholes who work there who leak things to the media. However, the FAA doesn't give a damn about advanced technology and didn't lift a finger to actually figure out whether the companies they were giving launch licenses to for R&D projects actually had the capabilities they claimed they were testing for. For all the FAA and the Pentagon knew, Musk could've just been lying about the intent of his project and would just claim that anomalies in flight prevented the cool tech he was promising from actually being tested.