"Trust me on this one, Captain. If anyone knows how to survive political changes, it's me."
In 2259, Welles was an influential figure in the new Clark administration and alongside Frederick Lantze was actively involved in the formation of the Ministry of Peace and its Nightwatch Division. Late in the year, he visited Babylon 5 with Lantze to meet the Nightwatch volunteers there and review their reports. He also confronted those who did not send reports, like Zack Allan. He organized arrests of some individuals in the reports, such as Xavier Darabuto.
During the visit, Welles observed John Sheridan's defense of a Narn ship against the Centauri before the Non-Aggression Treaty Lantze was negotiating. He noted that what he did was legal, but they should have been informed sooner, given the Centauri negotiations.
In 2267, Mr. Welles, having survived the downfall of the Clark Regime as well as the disbandment of the Ministry of Peace and the Nightwatch organization, was still working for EarthGov on behalf of the Political Affairs Office. He was assigned to oversee changes to the Excalibur Expedition's public image after concerns were raised as to how mission was being perceived by Earth's general populace. The changes were purely cosmetic and limited mostly to adjusting the ship's internal colour scheme and designing a unique variant of the Earthforce uniform.
While aboard the Excalibur, Welles and several crewmen became unwilling hosts to a group of non-corporeal Mind-Altering aliens accidentally brought over from a derelict alien ship. The alien inhabiting Welles largely assumed the role of speaker for the alien in their interactions with Captain Matthew Gideon. The aliens demanded to be transported to a colony world, or they would begin executing the crew members they inhabited. The Excalibur eventually successfully expelled the aliens by decompressing the room they had gathered in, forcing them all to transfer their consciousness into Welles, where they in turn transferred themselves to the body of security officer Stewart Greenberg, unaware that an injury had left Greenberg brain dead, and thus his body unable to move. With the aliens gone, Welles and the inhabited crew members made a full recovery.