Who knows with Trump. He might very well fire Mueller if he gets worried enough. He'll almost certainly at least refuse any subpoenas by him a la Nixon.
But if he does, or especially if he fires the special prosecutor, which technically he can do if I read the law correctly, then he may be subpoenaed by Congress or the Supreme Court. Technically he could refuse either, but Congress would then have grounds to begin impeachment proceedings and eventually remove him from office if both houses have the votes, at which point he becomes a private citizen again.
Whether he, as President, can pardon himself from prosecution as a private citizen is probably so unprecedented that it would likely be heard by the Supreme Court as a matter of constitutional law. But it's all moot if Congress won't impeach him, and given the way Congressional Republicans have been fawning and kowtowing to Trump and his cronies, it's pretty clear they won't even if Mueller lasts long enough to find something damning. But that could be just in time for midterm elections next year so...
It amazes me that the Founding Fathers toyed with the idea of making the President even more powerful an office than it already is.