TO AMERICANS who assume that Egypt, as a recipient of $1.3 billion in annual U.S. military aid, is a friendly ally, the case of Aya Hijazi might seem puzzling. The 29-year-old American, who grew up in Falls Church and graduated from George Mason University, has been imprisoned in Cairo since May 1, 2014 — 960 days — on what both Egyptian and international human rights groups say are flagrantly trumped-up charges. Her trial, postponed seven times, did not even begin until last month, making her continued imprisonment illegal under Egypt’s own laws. Yet the government of Abdel Fatah al-Sissi has brusquely rejected calls by the White House and State Department for Ms. Hijazi’s release.

If this does not sound like the behavior of an ally, it is because it isn’t. Ms. Hijazi’s case reveals a contradiction at the center of U.S.-Egyptian relations: Even while accepting U.S. subsidies, Mr. Sissi is waging what he calls “fourth-generation warfare” against what he considers to be Washington-sponsored subversion in his country. According to the regime’s conspiracy theories, U.S.-backed nongovernment groups are bent on overthrowing the government, dividing Egypt into pieces, delivering it into the hands of Israel or the Muslim Brotherhood — or maybe all of those things.

In other words, Ms. Hijazi is imprisoned not in spite of her American citizenship, but because of it. After meeting and marrying an Egyptian in Cairo, Ms. Hijazi joined with him to create a charity organization that aimed to help Cairo’s numberless street children. That placed her in the crosshairs of state security operatives, who have been conducting a sweeping crackdown on all nongovernment organizations with Western connections.

Ms. Hijazi, her husband, Mohamed Hassanein, and six other people connected to their Belady Foundation were charged with sexually abusing the children in their care and enlisting them in anti-government demonstrations. No evidence has been presented to back up these claims, other than purported statements by the children; a forensic examination found no sign of abuse. The trial was repeatedly delayed on the pretext that time was needed to study the contents of laptops seized from the foundation’s office. Yet when the study was presented, it contained nothing to back up the charges.

When the trial finally got underway last month, police who arrested Ms. Hijazi testified that they could not remember why she was taken in. The children who allegedly were abused were said to be missing and unable to testify. The laptops contained no photos of the children, nor of demonstrations. Yet rather than dismiss the case, or grant the defense’s motion to release Ms. Hijazi and her co-defendants on bail, the judge ordered more hearings, beginning this Saturday.

In addition to the Obama administration, several members of Congress, including Sen. Benjamin L. Cardin (D-Md.) and Rep. Don Beyer (D-Va.), have been pressing for Ms. Hijazi’s release. But the worry is that the court will contrive to extend the trial until January, when the Trump administration takes office. Donald Trump, who has been assiduously courted by the Sissi regime, has shown no hint of interest in its human rights violations. Ms. Hijazi’s case will test whether Mr. Trump’s “America First” rhetoric reaches as far as to protect Americans who are singled out for persecution by supposed U.S. allies.