On 20 April 1940Josef Terboven, newly appointed as Reichskommissar for the occupied Norwegian territories, selected Wegener to serve as his deputy. From the start Wegener was hostile to the notion that Vidkun Quisling should take a leading role in the new government, instead favouring the idea that the Nazis should establish their own administrative system in Norway. Eventually when it was decided to include Quisling he established the Einsatzstab Wegener, which placed pro-Wegener men in each branch of the Nasjonal Samling, both to improve the organisation of what had been a minor party and to ensure complicity with the demands of the governing Nazis. He left Norway in 1942 when took over as Terboven's number two.
Gauleiter
, Gauleiter of Weser-Ems, died on 15 May 1942 after a stroke and on 26 May Wegener was appointed to succeed him. On 27 May Wegener was also named to replace Röver as Reichsstatthalter of the states of Bremen and Oldenburg. He served in these positions through the end of the war in Europe. Soon after his appointment Wegener produced an internal document, the "Wegener Memorandum", in which it was said that the Nazi Party should be purged of much of its vast membership and instead be reorganised as an elite group to provide leadership for future generations of Germany. To this Wegener proposed a reorganisation of the Hitler Youth to bring it under the control of the party bureaucracy rather than the state. This new Hitler Youth would provide all the future membership of the Nazi Party with most existing party members absorbed into the Sturmabteilung, which was to be reconstituted as a veterans organisation. His plan also included a strengthening of the role of the Nazi Party Chancellery and this occurred in the following months as Wegener's old mentor Bormann was given greater power at the expense of the Reichsleiters of the party and the Reichsministers of the cabinet. In July 1944, when Joseph Goebbels was made Plenipotentiary for Total War, Wegener was made his head of administration. This made him one of only two permanent staff members appointed at national level.
Post-war
Wegener spent time in prison for his involvement in civilian deaths during his time in Bremen before finding work as a salesman in Sinzheim and then Wächtersbach. According to British secret service files Wegener was also involved with an underground group of ex-Nazi Party members, organised by Werner Naumann, which was involved in attempts to infiltrate the Free Democratic Party.