Nobody with any common sense believes the Warren Commission explanations for the Kennedy assassination. Nobody with any common sense believes that the reason we went into Iraq was to liberate Iraqis from Saddam's despotism. There are the official cover stories, and then there's what really happened.
The problem lies in that while the cover stories rarely pass the laugh test, you can never be sure about what is really going on. You can speculate and come up with the most elaborate conspiracy theories, but you never really know. You can do a lot of research, and maybe you can get a bigger collection of dots to connect than the next guy. But about too many subjects, usually the ones that matter most to us, there's always someone with more dots or someone else who has the same dots as you but connects them differently. People who do it well, who are more often right than wrong in their judgments have what the Greeks called 'phronesis' or practical wisdom.