Let's see.
1. The nose gear doors and a first-class passenger seat were among the very first things lost from the plane.
2. NTSB agents were caught altering the data about where they were found in the ocean, "otherwise, we wouldn't have been able to explain their location to [NTSB Chair] Hall."
3. More than 100 people saw a "flare" or "streak" rise FROM GROUND LEVEL prior to the mid-air explosion.
4. Radar data was leaked very early in the investigation that shows a mystery object in the air well away from TWA 800, prior to its destruction.
5. Radar data also showed objects leaving the aircraft at Mach 2.2 - the speed of a SAM, not the speed of objects expelled from a fuel-air explosion.
6. The search field the FBI used included a broad swath to the south of the explosion, but not to the north, indicating they expected to find objects there, in contrast to their publically-stated position that there was "no evidence of a missile."
7. They also left a book on one of the shrimp trawlers they hired that showed exactly what they were looking for - the battery pack for a SAM. This too happened when they were telling the public that there was "no evidence" of a missile.
8. The last line of the flight data recorder was deleted from one public hearing, after being showed at the first hearing. The data was consistent with a SAM attack.
9. Pieces of wreckage found to contain traces of explosives were taken away by the FBI and not returned to the NTSB - and some never appeared on the NTSB database of recovered parts.
10. Traces of explosives that were found were explained away as having come from a "dog training exercise" despite the fact that the accident aircraft departed, fully loaded with passengers, fuel and crew some 20 mins after the alleged dog training exercise took place. (Kind of quick for a 747, no?)
11. Traces of explosives were found on exterior aircraft surfaces, far from the passenger compartment where dog training exercises took place.
12. Clinton announced that he would "make a statement" about the disaster, and he later attended memorial for the victims - both extremely unusual, and which didn't occur for other accidents like Swiss Air #110 and the ValuJet crash in Florida.
13. Seats near the front of the plane had a "red residue" that wasn't found elsewhere on the plane.
14. James Sanders was prosecuted for removing two swatches of seat cloth containing this residue and having it tested - under the anti-souvenir law. This despite the fact he took the pieces for testing, and not to obtain a sovenir, and this too in light of the fact that FBI lead man James Kallstrom DID take pieces obtained from the wreckage, and DID give it to another (a victim's family member) as a souvenir.
15. The NTSB lied about the outcome of their tests of this red residueunder oath in a court of law.
16. The FBI removed all traces of red residue-tinged seat material from the wreckage reconstruction soon thereafter.
17. "Virtually all the victims had shrapnel" said the medical examiner. This is not the case in most airplane crashes.
18. There were "fist-sized holes" in some tray tables, and the damage was the worst in the first-class cabin. Again, if the center wing tank exploded first, how does the damage get to the first class without first destroying the main cabin?
19. There was a remarkable lack of interest in eyewitness testimony. Many witnesses weren't contacted within months of the accident, and the statements that they made weren't used by the FBI nor by NTSB to triangulate the apparent origin of whatever it was they saw; this task was first accomplished by independent researchers.
20. Witness testimony wasn't even mentioned at the hearings about the crash.
21. Why did the CIA, which is the foreign intelligence service, make a video about the crash of a domestic airline crash in American waters, for distribution to the general US public on the evening news? It's only purpose was to discredit witness accounts of having seen a missile, and among the few words used to caption the film, "Witnesses did NOT see a missile" was one such caption.
22. The animation claimed an aerodynamically impossible zoom-climb scenario, in which the ascending airliner shot up an additional 3000 feet, and which was mistaken by people on the ground for a missile. Except that many people saw things ascend FROM THE SURFACE. In any case, if a plane loses its nose, it becomes tail-heavy, and rotates in pitch rapidly until a stall occurs, without any gain in altitude. This isn't what the CIA animation represented had occurred.
23. The NTSB produced two animations and the CIA produced a third. All three are inconsitent with one another and with physical law. The NTSB later admitted that no "zoom-climb" was necessary to explain any aspects of its own version of the crash, nevertheless, all three animations went out of their way to posit a zoom-climb in order to make the case that people mistook that event for a missile. So apparently the only purpose of the climb was to discredit the witnesses. Why?
24. The TWA 800 investigation was overseen by Clinton administration officials.
25. Jet A doesn't burn and certainly doesn't explode unless it has been misted.
26. The NTSB admits it can't find any source of energy for the spark that allegedly set off the CWT explosion.
27. The Bruntingthorpe tests used flammable gases (e.g. hydrogen) to "simulate" the explosion ... why not use Jet-A vapor?
28. The results of that test explosion were so different from that seen from TWA 800 that the results were suppressed and continue to be suppressed.
29. A national guard pilot took a piece of wreckage to another airport for transportation to the FBI lab in Washington. It had what looked like bullet holes that went right through the thickest part of the leading edge of the main wing - in and out, and tested positive for explosives. This is inconsistent with the CWT explosion scenario.
There's nearly thirty facts for you. I could probably come up with more if I thought about it at length. If one or two were true, it would be curious. If ten were true, there would be serious questions about the scenario. Instead, I have offered nearly 30. I can't give you links for all of them right now - pick a few which, if you were convinced they were true, would satisfy you that the investigation was a cover-up, and I'll follow those up.