Poland
In September 1939 during the German attack on Poland, which launched the Second World War, Michalczyk was part of the SS force from Oppeln that marched into Częstochowa. In Poland, he led a 70-man SS unit that, in addition to guard duties, trained the "Volksdeutscher Selbstschutz" in Piotrków Trybunalski, as well as the Opoczno and Rawa districts. This paramilitary organization, made up of ethnic Germans living in Poland, was used as an auxiliary police force and involved in the deportation and murder of Jews and ethnic Poles. In 1940 Michalczyk, embarrassed by his Polish-sounding surname, officially changed it to Michalsen.
Initially, Michalsen was assigned to the staff of SS-Oberführer Fritz Katzmann, the SS and Police Leader (SSPF) in the Radom District of the General Government. In August 1940, he transferred to the staff of SS-Brigadeführer Odilo Globočnik, the SSPF of the Lublin District. Michalsen ran a camp for mainly Jewish forced laborers charged with building fortifications along the German-Soviet demarcation line. After the German attack on the Soviet Union, Globočnik was assigned to set up SS and police bases (Polizeistützpunkte) in the newly conquered areas of the Soviet Union and Michalsen was appointed head of the unit in Riga. Michalsen was present when the Riga Ghetto was partially cleared on 30 November 1941 and approximately 13,000 people were shot in the forest of Rumbula.
Michalsen was promoted to SS-Hauptsturmführer on 30 January 1942 and, in the early summer, returned to Lublin. At that time, following the Wannsee Conference, Globočnik was organizing Operation Reinhard, the systematic murder of all Polish Jews. In Treblinka, Belzec and Sobibor, extermination camps were set up for industrial-scale murder utilizing gas chambers. On 21 July 1942, a cadre of officials from Globočnik's office, including Michalsen, SS-Sturmbannführer Hermann Höfle and SS-Sturmbannführer Ernst Lerch arrived in Warsaw at the onset of the Grossaktion Warsaw, the expulsion of the Jews from the Warsaw Ghetto. Beginning on 27 July, approximately 7,000 Jews per day were transported by train for alleged "resettlement" to the east, however, the true destination of the deportations was the Treblinka extermination camp. During this time, Michalsen was deployed at the Umschlagplatz, where the victims boarded the transports. The deportations lasted until 21 September 1942, and it is estimated that around 265,000 Warsaw Jews were murdered in this fashion.[5]
In addition to the operation in Warsaw, Michalsen, together with others in Lublin cadre, played a leading role in the evacuation of the ghettos in Otwock, Wołomin, Piaski, Międzyrzec Podlaski and Włodawa. During the final destruction of the Warsaw Ghetto in April and May 1943, Michalsen organized the relocation to a site in Lublin of the Többens and Schultz factories that employed thousands of forced laborers. By this time, Michalsen was considered one of the foremost SS experts in the liquidation of ghettos. Between August 16 and 23, 1943, Michalsen was involved in the liquidation of the Białystok Ghetto where at least 30,000 people were deported to Treblinka and Auschwitz. In recommending that Michalsen be promoted to SS-Sturmbannführer on 11 February 1945, Globočnik wrote: "M[ichalsen] took part in the R[einhard] operation in an independent and decisive manner and, for example, had a decisive influence on the heavy fighting in Warsaw, and also cleaned Bialystok in 5 days."
Italy
Following the armistice between Fascist Italy and the Allies, now SS-Gruppenführer Globočnik on 13 September 1943 was promoted to the newly created post of Higher SS and Police Leader (HSSPF) in the Operational Zone of the Adriatic Littoral, with headquarters in Trieste. He brought along several of his trusted underlings, including Michalsen, Höfle and Lerch. In Trieste, Michalsen worked in the HSSPF headquarters staff, as head of the personnel section. He was also involved in fighting partisans in Istria and led the SS and police forces in a number of Italian cities, first in Fiume (today, Rijeka), later in Pola (today, Pula). Finally, on 27 October 1944, he was officially given the post of SS and Polizeigebietkommandeur (Police Area Commander) in Trieste, which was the site of the Risiera di San Sabba, a concentration and transit camp where it is estimated that over 3,000 persons were killed.