A Peruvian man identified in court filings as “John Doe” is safe for now after a federal appeals court reiterated that its decision overturning the Trump administration’s third country removal policy took effect immediately. Flight data, however, showed ICE charter activity in Africa hours later, raising questions about whether other immigrants faced unlawful removal.

The man has judicial protection from deportation to Peru and has been held in ICE custody in Massachusetts since July, according to one of his attorneys. On Tuesday, the Department of Justice asked a federal judge to lift her stay so ICE could transfer him for removal to the Central African Republic.

The First Circuit Court of Appeals had struck down the Department of Homeland Security’s third country removal policy in the D.V.D. v. Department of Homeland Security case. A Department of Justice attorney nevertheless argued that the ruling was not yet controlling because the appeals court had not issued its official mandate to the lower court.

Under that theory, the stay on the lower court’s ruling remained active, and ICE could continue subjecting Doe to third country removal. Put plainly, the Department of Justice claimed the policy could continue until the paperwork caught up.

Attorneys representing the D.V.D. plaintiffs filed an emergency motion Wednesday evening seeking clarification. They cited the Prospect’s reporting about Doe and said they had learned that an impending ICE flight would leave Alexandria, Louisiana, with planned removal stops in Rwanda, Burundi, and the Central African Republic.

Shortly before midnight, the appeals court answered with a response of three sentences. It declared, “Consistent with this court’s September 18, 2026, Judgment, the March 16, 2026, stay pending appeal is dissolved.”

That meant the lower court’s decision finding the policy unlawful was in effect. During an emergency hearing Thursday morning, a Department of Justice attorney continued pressing the mandate argument, according to Doe’s attorney Mary Holper.

The judge refused to disregard the appeals court’s clarification. Although no final ruling was issued on Doe’s request for release, the judge also declined to lift the stay preventing his removal from his current location.

ICE and DHS did not respond to requests for comment about the rulings. DHS instead delivered a pair of bizarre responses to earlier questions about Doe’s case and flight data showing an ICE charter aircraft preparing to fly to Ghana.

An unidentified DHS representative replied, “Please provide an A# or DOB,” requesting Doe’s alien number or date of birth even though neither was required to address the court filings or flight information. DHS spokesman Micah Bock later wrote, “When you fail to provide us with the necessary information to verify your claims, you’re wasting our time, which is ironic considering we at DHS can’t think of a bigger waste of time than writing for the American Prospect .”

ICE complied with the order preventing Doe’s removal from Massachusetts, but its deportation machinery continued moving. When the clarification was filed at 11:36 p.m. Eastern time, a Gulfstream V chartered by ICE was crossing the Atlantic toward West Africa.

The aircraft was the same plane previously identified as having a flight plan to Ghana, which has accepted more third country nationals from ICE than any other African country. Flight data showed it landed in Ghana at approximately 7:53 a.m. local time, or 3:53 a.m. Eastern time, before landing three hours later in Liberia.

At the time of publication, that aircraft was in Dakar, Senegal, where ICE charter crews typically stop for crew rest. DHS, ICE, and Talon Air, the charter operator based in Farmingdale, New York, did not answer questions about the ruling or whether third country nationals were aboard.

A second aircraft, a Gulfstream IV operated by Journey Aviation, left Alexandria at 12:32 a.m. local time Thursday, about two hours after the clarification. Roughly three hours later, it landed at the United States military base at Guantanamo Bay, Cuba, marking Journey’s first trip there during its 18 months of ICE flights.

Approximately 12 Somali men in ICE custody have been imprisoned at Guantanamo Bay since last month, according to Mother Jones and other news organizations. The aircraft later landed in San Juan, Puerto Rico, a common fuel stop for ICE charter flights heading toward Africa, and was flying east over the Atlantic at publication time.

Journey told the Prospect that it does not comment on charter flights and directed questions about possible removals to its client. The two aircraft are leased from billionaires with ties to President Trump and have made at least two dozen ICE removal stops since last October, including third country removals to Africa, according to an analysis of public flight data.