This timeline considerably expands an earlier outline and, I hope, provides enough context for understanding the command transition from Pope to McClellan.
8/30/62 (no time noted). McClellan to Barnard. Responding to Barnard’s question about their respective jurisdictions, McClellan says "Of course, everything is under your charge as usual." [Everything = the D.C. forts.] (OR)
9/1/62 1:30 a.m. Halleck to McClellan: "… the falling back on the line of works must necessarily be directed…" (OR)
9/1/62 (no time noted). Halleck to McClellan: Pope has been ordered to fall back to the line of fortifications. (OR)
9/1/62 (no time noted). GBM, Lincoln and Halleck meet in Halleck’s office. They draft the order placing GBM in command of the Washington defenses (Lincoln Day by Day, citing the Washington Star. And the Philadelphia News.)
9/1/62 (no time noted). In the meeting with Lincoln and Halleck, "the general in chief instructed me verbally to take command of its defenses expressly limiting my jurisdiction to the works and their garrisons, and prohibiting me from exercising any control over the troops actively engaged…" (McClellan, Report)
9/1/62 (no time noted). McClellan meets with Lincoln about "unkind feelings" towards Pope. In his letter to Porter urging cooperation, dated by Sears as 9/1 at 5:30 pm, (Waritme Papers of GBM), McClellan says "I am in charge of the defenses of Washington…"
9/1/62 2:00 pm. In notes that appear to be taken from a letter sent to his wife annotated with this date and time, McClellan says "I have been placed in command of Wash and all the garrison…"
9/2/62 (no time noted). McClellan, Halleck, and Lincoln meet. (Prime and McClellan, McClellan’s Own Story)
9/2/62 (morning). Lincoln encounters Chase and gives him the same story as recorded by McClellan's letters. Chase enters in his diary that McClellan has been given the Washington defenses. (Life of Chase by Warden)
9/2/62, Lincoln briefs his cabinet at noon. Welles records events in his diary. McClellan has been given command of the Washington defenses. (Diary, Welles)
9/2/62 (no time noted). Halleck to Pope: "General McClellan has charge of all the defenses, and you will consider any direction, as to the disposition of the troops as they arrive, given by him as coming from me." (OR)
9/2/62 7:10 p.m. Pope to Halleck: Informs Halleck of his safe arrival within the defenses and says "I await your orders." (OR)
9/2/62 (no time noted). Townsend issues order in Halleck’s name: "… McClellan will have command of the fortifications of Washington and of all the troops for the defense of the capital." (OR)
9/2/62 (no time noted). Barnard to Marcy: sends a copy of his orders, just issued, relinquishing command of the forts. (OR)
9/3/62 (no time noted). Lincoln orders Halleck to organize a field army independent of the Washington defense forces. (OR)
9/3/62 (no time noted). Pope to Assistant AG Col. Kelton: "I do not exactly understand my situation here. Will you ask the general [Halleck] so I may know? Does McClellan command in chief on this side of the river [north of the Potomac] or do his functions only extend to designating the position [to be occupied by Pope’s units] … (OR)
9/3/62 (no time noted). Halleck to Pope: "General McClellan commands all the troops in the fortifications. A reorganization of an army for the field will be immediately made. Till then General McClellan, as senior and as commanding the defenses of Washington, must exercise general authority." (OR)
9/4/62 (no time noted). Pope to Halleck: Pope proposes a four-corps field army to Halleck, to be led by himself commanding Banks, McDowell, Reno, and Hooker. He says organization of this field army "can be completed in a day or two." (OR) [I do not know if McClellan became aware of this.]
9/4/62. Pope reads Lincoln his report of the recent campaign. Welles is present. Lincoln is disturbed. [Welles, Diary. Pope has been back from campaign for fewer than two full days!]
9/5/62 (no time noted). Pope to Lincoln: "I sent in to General Halleck this morning the official report I read to you yesterday. Justice to the living and the dead demand its immediate publication." "The blood of the slaughtered victims of this conspiracy cries from the ground.. In their name and the name of the country I ask that my official report be given at once to the public." "Will you please inform me of your decision that I may communicate it to the troops who are under my command who are clamoring for punishment to the offenders…" (Lincoln Papers)
9/5/62 11.30 a.m. Marcy to Pope: "The commanding general directs that you at once put your command in readiness to march, with three days' rations in haversacks, cartridge-boxes filled, and reserve ammunition in your wagons. You will please, when you are ordered to move from your present position, leave officers to forward to you such supplies as you are not not able to procure before."
9/5/62 12.5 p.m. Pope to Marcy: "Your order to have my command ready to march with three days rations received. Please inform me what is my command and where it is." (OR) [Could Marcy be referring to the four corps field army proposed by Pope to Halleck?]
9/5/62 12.5 p.m. [sic] Pope to Halleck: "I have just received an order to have my command in readiness to march with three days rations …" "Am I to take the field and under McClellan’s orders?" (OR)
9/5/62 (no time noted). Pope to Halleck: "It is understood, and acted on, that I am deprived of my command, and that it is assigned to McClellan. An order defining his exact status here as well as my own is necessary at once. I send you an official protest against his action." ["His action" = issuing orders to Pope.] Pope then urges Halleck to furnish his report of Bull Run II to the press "as soon as possible." (OR)
9/5/62 (no time noted). Halleck to Pope: "In the first place, I did not know what would be your command, the two armies having been virtually consolidated." "The troops at present are under McClellan’s orders, and it is evident that you cannot serve under him willingly." "We must all act together … reconcile differences … the ill feeling is very embarrassing …" (OR)
9/5/62 (no time noted). Halleck to McClellan: "The President has directed General Pope be relieved and report to the War Department." "I give you this … in advance of the orders…" (OR)
9/5/62 (no time noted). Halleck to Pope: "The Armies of the Potomac and Virginia being consolidated, you will report for orders to the Secretary of War." (OR)
9/5/62 (no time noted). Lincoln asks Burnside to command the field army while McClellan defends Washington. (Burnside by Marvel; cites Welles’ Diary) Burnside refuses.
9/5/62 Burnside and McClellan discuss the field army command around midnight as the 5th turns into the 6th. McClellan tells Burnside he would not want the field command if it is offered to him unless Stanton and Halleck resign. Burnside argues him out of this position after a long discussion. (Marvel, Burnside, citing journal extracts by Henry Raymond published in Scribners).
9/6/62. Pope is ordered to the Northwest. (OR)
9/7/62. McClellan takes to the field. "As the time had now arrived for the army to advance, and I had received no orders to take command of it, but had been expressly told that the assignment of a commander had not been decided, I determined to solve the question myself… " (Prime and McClellan, McClellan’s Own Story)