During World War II the Anhalter Bahnhof was one of three stations used to deport some 55,000 Berlin Jews between 1941 and 1945, about a third of the city's entire Jewish population (as of 1933). From the Anhalter alone 9,600 left, in groups of 50 to 100 at a time using 116 trains. In contrast to other deportations using freight wagons, here the Jews were taken away in ordinary passenger coaches which were coupled up to regular trains departing according to the normal timetable. All deportations went to Theresienstadt in Nazi-occupied Czechoslovakia, and from there to concentration camps.
Meanwhile, during World War II the Anhalter Bahnhof, like most of Berlin, was devastated by British and American bombs and Soviet artillery shells. A massive bombing raid on the night of 23 November 1943 badly affected the station, and caused so much damage to rail infrastructure further out that long-distance trains could no longer run, just a few local services. Two further major raids on 3 February and 26 February 1945 left the terminus with large sections of its roof missing, the rest unsafe and tottering, and no trains running at all. Many sections of the S-Bahn as well as the U-Bahn were also closed during the war due to enemy action, and the section through Anhalter Bahnhof was no exception.
The S-Bahn North-South Link, less than six years old, became the setting for one of the most contentious episodes of the final Battle of Berlin, in late April and early May 1945. With Hitler already dead, the remaining Nazi leaders resorted to increasingly desperate measures to slow the Soviet advance, whatever the consequences for their own citizens. Fearful that the Soviets might try to storm the centre of Berlin by coming through the underground rail tunnels, on 2 May the Nazi leaders ordered SS troops to blow up the bulkheads where the North-South Link passed beneath the Landwehrkanal. Altogether up to 26 km of tunnels and many stations were flooded by this action, most of which had been used as public shelters and also to house military wounded in hospital trains in underground sidings. No one knows how many people were drowned as figures are so diverse and unreliable. According to Soviet propaganda up to 15,000 may have lost their lives, but a more likely figure is two or three hundred.
A fragmentary train service resumed along the North-South Link on 2 June 1946 once massive repairs were well advanced (water had to be pumped out at the beginning). Full services recommenced on 16 November 1947, although repairs were not complete until May 1948. The services were extended further in 1951. Another interruption of services was caused by the uprising of 1953 in East Germany, no trains running between 17 June, the day of the uprising, and 9 July. Meanwhile, above ground, American servicemen had dismantled the surviving sections of the Anhalter Bahnhof's roof in March 1948, and a limited train service had begun operating again in August, with a few trains running out into the Saxony-Anhalt and Brandenburg regions, but it was not to last. The station's final demise was caused by the rapid collapse of relations between the Allied Occupying Powers which controlled Berlin and Germany as a whole. The Anhalter Bahnhof was served by trains arriving from places in Soviet-controlled East Germany, but the terminus was in West Berlin. An uncomfortable situation to start with, it eventually became a thorn in the Soviets’ side, and so on 17 May 1952, they switched all remaining trains to a station in their Eastern Sector, the Ostbahnhof, and the Anhalter Bahnhof was closed for good, although apparently not before detailed plans and an architect's model had been produced for a vast modern terminus on the site.
After lying derelict for more than eight years, apparently with some rusting tracks and signals still in situ, demolition was begun on 25 August 1960 and completed by 27 August. There was a considerable public outcry, but according to legend someone had put in a good offer for the bricks. The terminus did not vanish entirely, however, as the centre portion of the façade was allowed to remain standing.