The arrest was made on the 8th of February, 1862--forty-six days later.

The intervening circumstances nowhere involve Mr.Sumner in the remotest degree.
In answer to the call upon the President for information, Mr.
Lincoln sent a message to the Senate on the 1st of May, saying, "General Stone was arrested and imprisoned under my general authority, and upon evidence which, whether he be guilty or innocent, required, as appears to me, such proceedings to be had against him for the public safety." The President deemed it "incompatible with the public interest, and perhaps unjust to General Stone, to make a more particular statement of the evidence." After saying that General Stone had not been tried because the officers to constitute a court-martial could not be withdrawn from duty without serious injury to the service, the President gave this public assurance: "He will be allowed a trial without unnecessary delay: the charges and specifications will be furnished him in due season, and every facility for his defense will be afforded him by the War Department." This message on its face bears evidence that it was prepared at the War Department, and that Mr.Lincoln acted upon assurances furnished by Mr.Stanton.

The arrest was made upon his "general" authority, and clearly not from any specific information he possessed.
But the effect of the message was to preclude any further attempt at intervention by Congress.

Indeed the assurance that General Stone should be tried "without unnecessary delay" was all that could be asked.

But the promise made to the ear was broken to the hope, and General Stone was left to languish without a word of intelligence as to his alleged offense, and without the slightest opportunity to meet the accusers who in the dark had convicted him without trial, subjected him to cruel punishment, and exposed him to the judgment of the world as a degraded criminal.
Release from imprisonment came at last by the action of Congress, coercing the Executive Department to the trial or discharge of General Stone.