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Many far flung garrisons and especially islands were still in German hands at the end of the war in May 1945. Parts of Crete, Dunkirk, the Channel Islands, La Rochelle, St Nazaire and several other French ports, many other Greek islands to name just a few such territories. Clearly a part of the reason lies in Hitler's obsession with holding on to territory beyond the dictates of military logic (but not consistently; other islands, such as Corsica, were let go without a struggle), and a part of the reason lies in the Allies, sweeping all before them in battle, being happy to bypass these garrisons.

There are almost no equivalents in 1940/1 when the situation was (very broadly speaking) reversed. I can only think of Malta as an example. You might think there were numerous islands in Dalmatia, Norway, even Denmark, and certainly the Aegean (which could have been supplied from Egypt) which could have "held out". Of course there were mountainous areas of Greece and Yugoslavia which gradually became free of Axis control but none of them seem to have held out from the beginning.

Why the difference? Why didn't anyone try very hard in 1940/1 to hold out and equally why weren't the Germans happy to bypass garrisons as the Allies were three years later?

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These did not 'hold out', they were simply bypassed (with maybe some troops stationed in the vicinity to discourage attempts at breaking out and harassing the allied rear) as irrelevant towards the greater objectives of the campaign, Rome, the Ruhr, and Berlin. Once Germany surrendered formally, these garrisons laid down their weapons just as had garrisons of Dutch troops at Kornwerderzand in 1940, French troops stationed in places not yet attacked by the Germans ditto, etc. etc.
If you want 'holdouts', look no further than the Polish partisans who kept up a campaign against the Germans from deep forests for a long time starting in 1939.

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