After the change of government from Helmut Kohl to Gerhard Schröder in 1998, Mertes joined the editorial team of the German weekly Rheinischer Merkur and remained the newspaper’s foreign editor and deputy editor-in-chief until the end of 2002.
The newspapers and journals to which he contributed include Frankfurter Allgemeine Zeitung, International Herald Tribune, Neue Zürcher Zeitung, The Independent and several dailys belonging the Project Syndicate, as well as Dædalus, Foreign Affairs, Internationale Politik, Neprikosnovenny Zapás (Неприкосновенный запас),[3] Obshchaya Tetrad (Общая тетрадъ),[4] Politique étrangère, Prospect, The Washington Quarterly, Transit,[5] and the Israel Journal of Foreign Affairs.
In 2022, he and Vincent Fröhlich published the essay “Der neue Konspirationismus” (The New Conspiracism), exploring how digital platforms and fan communities create and disseminate conspiracy narratives.
In July 1989 he published, with his colleague Norbert J. Prill, a much-debated concept for a multi-speed Europe which was based on the idea that the European Community, considering the approaching end of the Cold War, should be prepared to include emerging new democracies from Eastern Europe and neutral countries such as Austria, Finland and Sweden; Mertes and Prill also pleaded for a stronger association of Israel and Turkey with the EC.
[7] During the 1990s Timothy Garton Ash, Michael Mertes and Dominique Moïsi wrote several „trilateral“ (British-German-French) pleas in favour of a combined eastward entlargement and institutional modernisation of the EU.
In 2006 he received, together with Rabbi Nathan Peter Levinson and Protestant Pastor Johannes Hildebrandt, the International Raoul Wallenberg Foundation's Roncalli Award for interfaith dialogue and understanding.