If the President is able to order an end to an investigation, what are the penalties for failure to execute his order? There is no such thing as a vaguely described power to command without consequences in place for failure to obey. In other words, the only powers Trump had to end this investigation were to pardon Flynn (he didn't) or fire Comey (he did) and hope that Comey's replacement doesn't just say no if Trump tries to order him to end it. Otherwise he'll be forced to fire that guy, too. Maybe the guy after that, until he finds one to agree to follow his suggestion....because it can't be called an order if the option to disobey it exists.

Trump's could write up an executive order ending the investigation, I suppose. That could be subject to judicial review, should the courts find anyone with legal standing to issue a challenge. and could (and almost certainly would) be stayed by the courts. In other words, the exact fate his travel ban met.