Whilst Halleck promised McClellan command of the joint force, which McClellan didn't believe, when McClellan's forces reached northern VA it was confirmed that they were all transferred to Pope's command.
Even after 2nd Bull Run, the intent was for Pope to command the army in the field, and McClellan was only assigned to the defences of Washington.
"
In the middle of the forenoon [of 1st September] Halleck sent a message to McClellan that he was anxious to see him, McClellan went to Washington and Halleck gave him verbal instructions to take command of the defenses, expressly limiting his jurisdiction to the works and their garrisons, and prohibiting him from exercising any command over the troops actively engaged in front under Pope. At this interview McClellan told Halleck what he had reason to know to be the true state of affairs, that the army had been defeated and had lost confidence in Pope. Halleck doubted the accuracy of McClellan's information and believed in the statements of Pope, although Pope had substantially confirmed all that McClellan had said. McClellan then plainly told him he ought to go to the front in person and see for himself the true condition of affairs; Halleck excused himself on the ground that he was too much occupied with office affairs to permit him to go. McClellan reminded him that there could be no duty so important for the general-in-chief of the armies as to know the condition of the chief army of the country, then actually fighting for the safety of the capital, and that his first duty was to go out and see for himself how matters stood, and, if need be, assume command in person. Halleck merely repeated his reply, and McClellan then urged that General Cullum, the chief of staff, might be sent, but Cullum excused himself, he also had a great deal of office work to do. Then McClellan asked that Colonel Kelton, adjutant-general to Halleck, might be sent, and Kelton cheerfully offered to go, and to go immediately, and Halleck consented.99"
Carman, Ezra A.. The Maryland Campaign of September 1862: Volume III - Shepherdstown Ford and the End of the Campaign (pp. 184-185). Savas Beatie. Kindle Edition.
Carman's chapter on this matter is extremely inciteful. Both in the crisis of August-September '62, and July-August '64 Halleck refused to take personal command of the forces near Washington.
Bringing the