WASHINGTON — When former Venezuelan leader Nicolás Maduro appeared in federal court in New York this week and entered a plea of not guilty to sweeping drug-trafficking and terrorism-related charges, the moment marked more than the start of a criminal case. It opened a new phase of legal and political uncertainty for the Trump administration, whose dramatic military operation to seize Mr. Maduro is now under intense judicial examination.

The arraignment, overseen by Alison Nathan, came just days after U.S. forces captured Mr. Maduro in a weekend raid that administration officials described as a decisive blow against international narcotics networks. President Donald Trump hailed the operation as a historic assertion of American power. But within 48 hours, the tone shifted.

Speaking to reporters aboard Air Force One, Mr. Trump acknowledged that the prosecution ahead would be, in his words, “a slog,” signaling an awareness that the legal aftermath of the operation could be as consequential as the raid itself.

A Judge With a Familiar Role

Judge Nathan is no stranger to cases that test the outer limits of executive authority. In prior proceedings involving Mr. Trump, including litigation connected to his New York hush-money case, she rejected arguments that sought to characterize personal conduct as protected “official acts.” Legal analysts note that her rulings have consistently emphasized a narrow interpretation of executive immunity.

That record has heightened attention around her role in the Maduro case, particularly as defense attorneys move quickly to challenge not just the charges but the circumstances of Mr. Maduro’s capture.

On Monday, Judge Nathan ordered Mr. Maduro to provide sworn testimony next week, an unusual step at this early stage. While such testimony does not presume guilt or innocence, it suggests the court is prepared to examine closely how the defendant was brought into U.S. custody and whether constitutional and statutory requirements were met.

Legal Challenges to the Raid

Mr. Maduro’s legal team has filed a series of motions questioning the legality of the military operation that led to his arrest. Central among them is a challenge under the War Powers Resolution, arguing that the president lacked authority to conduct a unilateral raid without congressional approval or a clear, imminent threat to the United States.

Defense lawyers are also seeking suppression of evidence obtained during the operation, contending that if the raid is deemed unlawful, any materials seized would be inadmissible in court.

“These are not procedural technicalities,” said a former federal prosecutor who reviewed the filings. “If a judge finds the initial seizure violated U.S. law, the entire case could be compromised.”

The Justice Department, led by Attorney General Pam Bondi, has defended the operation as lawful and necessary, citing what it describes as overwhelming evidence that Mr. Maduro oversaw a massive drug-trafficking enterprise with links to designated terrorist organizations. Prosecutors allege that billions of dollars’ worth of cocaine moved through networks controlled by Venezuelan officials during Mr. Maduro’s tenure.

Political Reverberations in Washington

The court proceedings are unfolding as lawmakers in Washington debate the scope of presidential war powers. Several members of Congress from both parties have demanded classified briefings on the operation, and some Democrats have renewed calls for legislative action to constrain unilateral military deployments.

Should Judge Nathan determine that the raid exceeded presidential authority, the ruling could reverberate well beyond the courtroom. A finding that the operation violated the War Powers Resolution would bolster congressional efforts to reclaim oversight and could provide political ammunition for critics who argue that Mr. Trump has repeatedly pushed beyond constitutional limits.

Conversely, if the judge allows the prosecution to proceed without restriction, the administration would gain legal validation for one of its most aggressive foreign policy actions to date.

The Stakes of Testimony

Mr. Maduro’s forthcoming testimony is expected to focus on the circumstances of his arrest and the substance of the charges. Legal experts caution that such testimony could expose details of military planning, intelligence assessments, and internal deliberations within the administration.

“Once those facts are on the record, they don’t disappear,” said a constitutional law scholar. “They become available not just to the court, but to Congress, historians, and the public.”

That prospect has raised concern among administration allies, who worry that disclosures could complicate ongoing diplomatic and security efforts in the region.

A Broader Pattern

For critics of the president, the Maduro case fits a familiar pattern: a bold executive action followed by protracted legal battles that test its legitimacy. Supporters counter that decisive action is precisely what voters demanded, and that courts should not second-guess national security judgments.

What is clear is that the administration’s Venezuela strategy is no longer defined solely by the success of a military raid. It is now bound to judicial rulings that will determine whether the operation stands as a precedent for future interventions — or a cautionary tale about constitutional limits.

As Mr. Maduro remains in federal custody awaiting further hearings, the balance of power among the presidency, Congress, and the courts is once again being tested. Judge Nathan’s decisions in the coming weeks are likely to shape not only the fate of one defendant, but the contours of American executive authority in an era of heightened global confrontation.

For President Trump, the case has already shifted from a moment of triumph to a complex legal contest — one in which the outcome may hinge less on military success than on the judgments of a federal court.