Germany subsequently invaded Denmark and Norway, the Netherlands, and France, and began bombing Great Britain in preparation for Operation Sea Lion, the planned invasion of the United Kingdom. On 21 June 1941, the day before invasion of the Soviet Union, Himmler commissioned the preparation of the Generalplan Ost (General Plan for the East); the plan was finalised in July 1942. It called for the Baltic States, Poland, Western Ukraine, and Byelorussia to be conquered and resettled by ten million German citizens. The current residents—some 31 million people—would be expelled further east, starved, or used for forced labour. The plan would have extended the border of Germany a thousand kilometres to the east (620 miles). Himmler expected that it would take twenty to thirty years to complete the plan, at a cost of 67 billion Reichsmarks. Himmler stated openly: "It is a question of existence, thus it will be a racial struggle of pitiless severity, in the course of which 20 to 30 million Slavs and Jews will perish through military actions and crises of food supply."
In late 1941, Hitler named Heydrich as Deputy Reich Protector of the newly established Protectorate of Bohemia and Moravia. Heydrich began to racially classify the Czechs, deporting many to concentration camps. Members of a swelling resistance were shot, earning Heydrich the nickname "the Butcher of Prague". This appointment strengthened the collaboration between Himmler and Heydrich, and Himmler was proud to have SS control over a state. Despite having direct access to Hitler, Heydrich's loyalty to Himmler remained firm.
With Hitler's approval, Himmler re-established the Einsatzgruppen in the lead-up to the planned invasion of the Soviet Union. In March 1941, Hitler addressed his army leaders, detailing his intention to smash the Soviet Empire and destroy the Bolshevik intelligentsia and leadership. His special directive, the "Guidelines in Special Spheres re Directive No. 21 (Operation Barbarossa)", read: "In the operations area of the army, the Reichsführer-SS has been given special tasks on the orders of the Führer, in order to prepare the political administration. These tasks arise from the forthcoming final struggle of two opposing political systems. Within the framework of these tasks, the Reichsführer-SS acts independently and on his own responsibility." Hitler thus intended to prevent internal friction like that occurring earlier in Poland in 1939, when several German Army generals had attempted to bring Einsatzgruppen leaders to trial for the murders they had committed.
Following the army into the Soviet Union, the Einsatzgruppen rounded up and killed Jews and others deemed undesirable by the Nazi state. Hitler was sent frequent reports. In addition, 2.8 million Soviet prisoners of war died of starvation, mistreatment or executions in just eight months of 1941–42. As many as 500,000 Soviet prisoners of war died or were executed in Nazi concentration camps over the course of the war; most of them were shot or gassed. By early 1941, following Himmler's orders, ten concentration camps had been constructed in which inmates were subjected to forced labour. Jews from all over Germany and the occupied territories were deported to the camps or confined to ghettos. As the Germans were pushed back from Moscow in December 1941, signalling that the expected quick defeat of the Soviet Union had failed to materialize, Hitler and other Nazi officials realised that mass deportations to the east would no longer be possible. As a result, instead of deportation, many Jews in Europe were destined for death.
Nazi racial policies, including the notion that people who were racially inferior had no right to live, date back to the earliest days of the party; Hitler discusses this in Mein Kampf. Somewhere around the time of the German declaration of war on the United States in December 1941, Hitler finally resolved that the Jews of Europe were to be "exterminated." Heydrich arranged a meeting, held on 20 January 1942 at Wannsee, a suburb of Berlin. Attended by top Nazi officials, it was used to outline the plans for the "final solution to the Jewish question". Heydrich detailed how those Jews able to work would be worked to death; those unable to work would be killed outright. Heydrich calculated the number of Jews to be killed at 11 million, and told the attendees that Hitler had placed Himmler in charge of the plan.
Initially the victims were killed with gas vans or by firing squad, but these methods proved impracticable for an operation of this scale. In August 1941, Himmler attended the shooting of 100 Jews at Minsk. Nauseated and shaken by the experience, he was concerned about the impact such actions would have on the mental health of his SS men. He decided that alternate methods of killing should be found. On his orders, by early 1942 the camp at Auschwitz had been greatly expanded, including the addition of gas chambers, where victims were killed using the pesticide Zyklon B. Himmler visited the camp in person on 17 and 18 July 1942. He was given a demonstration of a mass killing using the gas chamber in Bunker 2 and toured the building site of the new IG Farben plant being constructed at the nearby town of Monowitz. By the end of the war, at least 5.5 million Jews had been killed by the Nazi regime; most estimates range closer to six million. Himmler visited the camp at Sobibór in early 1943, by which time 250,000 people had been killed at that location alone. After witnessing a gassing, he gave 28 people promotions, and ordered the operation of the camp to be wound down. In a revolt that October, prisoners killed most of the guards and SS personnel, and 300 prisoners escaped. Two hundred managed to get away; some joined partisan units operating in the area. The remainder were killed. The camp was dismantled by December 1943.