Justice Department lawyers, confronting an onslaught of legal challenges, have made a case in court that expansive executive power inherent in the Constitution buttresses the lawfulness of President Trump’s aggressive unilateral actions.

Outside the courtroom, however, legal niceties have little to do with the strategies pursued by White House officials and their allies as they attack individual judges, question the legitimacy of the courts — and undermine the separation of powers that has been at the core of American governance since the nation’s beginning.

The two-pronged defense of Mr. Trump’s actions may be an understandable reaction to the run of successes that the president’s opponents have had in court. But it raises the prospect of a high-stakes confrontation between two branches of government that the nation’s founders designed as coequals: the executive and the judicial.

On Saturday, the number of active lawsuits in federal courts challenging administration actions reached 100. In 21 of those cases, judges had issued temporary restraining orders or preliminary injunctions, effectively stopping, at least for a time, parts of Mr. Trump’s second-term agenda.

Trial court judges have tried to block the unilateral firing of civil servants, the access that Elon Musk’s team has enjoyed to sensitive agency data, the relocation of transgender women inmates to men’s prisons, the pursuit of immigrants inside houses of worship, and the freezing of up to $3 trillion in federal funding to the states.

Late Friday, Judge Lauren J. King blocked a Trump administration plan to cut funding for hospitals that offer gender-transition treatment for people under 19. In her ruling, Judge King said the two Trump administration orders at issue were “a violation of the separation of powers.”

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