It's been blindingly obvious that Trump wants to stop the Mueller investigation, it's just that Ryan and McConnell, despite saying it should be allowed to continue, have blocked all votes in the House and Senate respectively on motions or bills that would protect it.
Mueller's a seasoned prosecutor, though, and he's taken steps to protect his work by farming out parts of it to other teams not necessarily under Trump's control. (For instance, I think he's been working with the New York Attorney General on matters that can be tried under that state's criminal law.)