To a degree, General Auchinleck was the cause of many of his own problems. For example, he was suspicious of the Minister of State, the Australian Mr. Casey, when in fact, Mr. Casey was very eager to be of help. Instead, Auchinleck kept Mr. Casey in the dark about events. But in any case, events were in flux during late June and early July 1942.
General Morshead got new orders on 30 June now putting his division at Alexandria, not Cairo. GHQ took the step of ordering the 26th Brigade Group to Amiriya. Brigadier Tovall had not yet received Morshead's orders about defending Cairo.
The withdrawal of the 8th Army to El Alamein and Rommel's initial attacks had panicked the administrative force in Egypt. They also planned for the Mediterranean Fleet to leave Alexandria, expecting a further collapse. The state of things is indicated by orders to prepare for withdrawal to the east and massive burning of documents. When reading General Morshead's notes of the meeting on 30 June, you can see that such a move to the east was thought to be a real possibility. That was because the collapse of the army from Gazala in May to the point in 30 June, no one had any confidence in the 8th Army or in army commanders. It turns out that General Auchinleck was a better man than anyone realized.
Part of Morshead's notes were that he was unsure if General Holmes had been captured. If he had, Morshead planned to assume command of Delta Force. In fact, General Holmes arrived and took command of Delta Force. On 1 July, when the 9th Australian Division moved to Alexandria, they were caught in traffic moving in the opposite direction. The panic in the area was very real. Traffic was moving against them "note-to-tail". There were tanks, guns, armored cars, and other vehicles, all moving out, ultimately to the east. To make matters worse, there was low visibility that cause accidents in the congested traffic. The Australians were caught in the traffic which moved very slowly due to the density. They were fortunate to not be attacked by German aircraft. The passengers and even drivers slept in their seats in their vehicles. This is base on the account in Vol.III of the Australian Official History.