The Constitution limits the federal judicial power to cases or controversies. When the government initiates and the defendant does not oppose dismissal of a guilty plea, the court loses subject matter jurisdiction because there is no longer a case or controversy to adjudicate. At most, the court would still have jurisdiction to impose sanctions for prior misconduct by an attorney or a party or witness.
By the way, an outstanding defense of that truth comes at the beginning of Scalia’s dissent in the DOMA case:
https://www.supremecourt.gov/opinions/12pdf/12-307_6j37.pdf