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Lieutenant-Colonel Sim had been told to dispose his forces in such a way as to protect the anchorage at Suda Bay from attack by a raiding force.  No-one was yet talking of an aerial invasion.  On the 7th November Sim's force was strengthened when the S.S. Brisbane Star arrived with the rest of the battalion's transport and the rear party.  H.M.S. York also brought the 2nd Battalion of the Black Watch as well as one heavy and one light battery of anti-aircraft artillery, and one field company of engineers.  The arrival of the British troops allowed the 5th Cretan Division to be released from Crete to the defence of mainland Greece.  On the 31st December, 1940, Lieutenant-Colonel Sim took an appointment in Egypt and was replaced as C.O. of the Battalion by Major A. Gilroy of the Black Watch.  Little was happening on Crete, but in April of 1941 the Allied forces in Greece were forced to evacuate the mainland, many of them heading for Crete.  While this evacuation was taking place the Battalion and the Black Watch were moved to the area around Heraklion.  Also, as a result of the evacuation from Greece the command of forces on Crete was placed in the hands of Major-General Freyberg, V.C.   

After this attempt there were no more paratroop drops on Heraklion, but the Germans did put a lot of effort into building up their forces outside the Heraklion perimeter.  The battalions role was now very much of digging in and holding the defence line, while putting out patrols as necessary, again from the battalion history;

One of the most successful leaders of the Battalion's patrols was Lieutenant D. McEwan.  He had joined the Battalion in March from the United Kingdom, having quite illegally avoided being posted to the Infantry Bas Depot in Egypt, and been made Intelligence Officer.  Somewhere he had picked up an English-speaking Greek soldier who had lost his unit.  This man, whom he attached to his Intelligence Section, proved invaluable as an interpreter.  With the local information which he gleaned from the villagers, Lieutenant McEwan and his picked band of men were able to penetrate far into the enemy-held country and bring back prisoners, booty and much useful data about the whereabouts of enemy forces.  Unfortunately, when leading such a patrol three days before the evacuation, Lieutenant McEwan ran into a machine-gun nest and was killed instantly.  This officer had only been with the Battalion a short time, but his ever-cheerfulness had made him popular with all ranks.  In the last few days he had proved himself a born leader and a very brave officer.

While the Germans were positioning forces around the Heraklion garrison, but before the encirclement was completed, a company of the Argyll and Sutherland Highlanders joined the defence, having made their way across the island from their landing on the south coast at Tymbaki.  The Germans were continually probing against the defences and the following is the last serious fighting in which the battalion took part before their evacuation from the island.

By now the position on the island had been lost, particularly in the west, and General Freyberg had ordered the evacuation of Allied forces from Crete.  The 2nd Battalion would leave from Heraklion port by sea.  At 06:00 on the 28th May Brigadier Chappel, who commanded the forces around Heraklion, issued orders for the evacuation of Heraklion.  The battalion, being nearest the harbour, would form an inner ring around it, and would fight to cover the embarkation of other units if the enemy followed them in.  If all went well, they would also be evacuated.  No one below the rank of officer was to be told of the evacuation before 20:00.  This secrecy extended to the hospital which had been set up in Knossos (site of the ancient palace).  The situation with the hospital was a little unique.  When the hospital fell into the area occupied by the Germans, they allowed it to continue operating as a joint hospital with red cross ambulances bringing in British wounded from Heraklion.  Captain Tucker was one of those left behind, and he later died of his wounds as a prisoner of war.

When the men were told of the impending evacuation, at 20:00, they were astonished "as to them the whole battle of the last ten days had seemed to have been eminently successful."  D Company, under Major J.H. Mott was the last to withdraw.  The ships taking them off eventually got away, later than planned, at 03:30 on the 29th May, and they were badly attacked en-route Alexandria as they knew they would be.  "Of the 4,000 troops in the evacuation from Heraklion, over one-fifth had been killed wounded or captured during the ill-fated voyage back to Egypt."