On 2 April 2009, Demjanjuk filed a motion in an immigration trial court in Virginia. The motion sought to reopen the matter of the removal order against him; that order of removal had been originally issued by an immigration court in 2005, had been upheld by the BIA on administrative appeal in late 2006, and was further upheld by the Sixth Circuit Court of Appeals; after these two appeals, the US Supreme Court had, as noted above, denied any review. On 3 April 2009, US Immigration Judge Wayne Iskra temporarily stayed Demjanjuk's deportation, but reversed himself three days later, on 6 April. As the Government noted, a motion to reopen, such as Demjanjuk's, could only properly be filed with the Board of Immigration Appeals (BIA) in Washington, D.C., and not an immigration trial court. The issuance of the stay by the immigration trial court was therefore improper, as that court had no jurisdiction over the matter. Accordingly, Demjanjuk re-filed his motion to reopen, and for an attendant stay, with the BIA. On 10 April, the BIA found there was "little likelihood of success that [Demjanjuk's] pending motion to re-open the case will be granted" and accordingly denied his motion for a stay pending the disposition of his motion to reopen. This removed any obstacles to federal agents seizing him for deportation to Germany.
On 14 April 2009, immigration agents removed Demjanjuk from his home in preparation for deportation. The same day, Demjanjuk's son filed a motion in the Court of Appeals for the Sixth Circuit asking that the deportation be stayed, which was subsequently granted. The Government argued that the Court of Appeals has no jurisdiction to review the decision of the Board of Immigration Appeals, which denied the stay. Demjanjuk later won a last-minute stay of deportation, shortly after US immigration agents carried him from his home in a wheelchair to face trial in Germany. The BIA denied Demjanjuk's motion to reopen his deportation case. On 1 May 2009, the Sixth Circuit lifted the stay that it had imposed against Demjanjuk's deportation order. On Thursday 7 May 2009, the United States Supreme Court, via Justice John Paul Stevens, declined to consider Demjanjuk's case for review, thereby denying Demjanjuk any further stay of deportation. Demjanjuk sued Germany on 30 April 2009, to try to block the German government's agreement to accept Demjanjuk from the US. The German Administrative Court rejected Demjanjuk's claim on 6 May.
Demjanjuk was deported to Germany, leaving Cleveland, Ohio, on 11 May 2009, to arrive in Munich on 12 May. Upon his arrival, he was arrested and sent to Munich's Stadelheim prison.
On 3 July 2009, prosecutors deemed Demjanjuk fit to stand trial. On 13 July 2009, prosecutors charged him with 27,900 counts of accessory to murder for his time as a guard at Sobibor. Demjanjuk was tried without any connection to a concrete act of murder or cruelty, but rather on the theory that as a guard at Sobibor he was per se guilty of murder, a novelty in the German justice system that was seen as risky for the prosecution. Some 35 plaintiffs were admitted to file in the case, including four survivors of the Sobibor concentration camp and 26 relatives of victims. The indictment made almost no mention of Demjanjuk's service at Majdanek or Flossenbürg, as these were not extermination camps.
Doctors restricted the time Demjanjuk could be tried in court each day to two sessions of 90 minutes each, said Munich State Prosecutor Anton Winkler. On 30 November 2009, Demjanjuk's trial, expected to last for several months, began in Munich. Demjanjuk arrived in the courtroom in a wheelchair pushed by a German police officer. Due to the long pauses between trial dates and cancellations caused by the alleged health problems of the defendant and his defense attorney Busch's use of many legal motions, the trial eventually stretched to eighteen months.