The man accused of plotting the attacks of Sept. 11, 2001, appeared in court on Thursday, watching silently as the prosecutor who had pursued his capital case since the beginning formally announced that a plea agreement had been reached that would remove the possibility of the death penalty.

The prosecutor, Clayton G. Trivett Jr., also gave the court the sealed and signed agreements between the prisoner, Khalid Shaikh Mohammed, and the Pentagon’s overseer of the war court cases.

Disclosure of the agreement in the court at Guantánamo Bay is the first step toward a sentencing hearing before a military panel, which could begin next summer.

Prosecutors who had negotiated the agreements with Mr. Mohammed and two accomplices, Walid bin Attash and Mustafa al-Hawsawi, disclosed the deal on Wednesday to family members of the nearly 3,000 people who were killed in the attacks.

The notices provided some details of the agreement that were not included in a brief Defense Department announcement, including an opportunity for Sept. 11 family members to submit questions to be posed to Mr. Mohammed and his co-defendants.

Mr. bin Attash and Mr. Hawsawi, who also reached plea agreements with prosecutors, did not come to court on Thursday. They each signed a document saying their absence was voluntary.