"We must tell you the truth, because the Minbari never tell anyone the whole truth."
- – Ambassador Juphar Trkider
During the Second Shadow War, Trkider replaced Vizak as the Drazi Ambassador to B5 and was among a group of League Ambassadors including the representatives of Vartas, N'chak'fah and Shir-shraba to hold a rally to publicly oppose Delenn's plan to attack Z'ha'dum. Delenn, who had been warned of the gathering by the Brakiri Ambassador Lethke Zum Bartrado, appeared and publicly argued against Trkider, to which he responded by inciting the angry crowd to silence her. The rally was cut short to the shock of all present when Sheridan, presumed killed at Z'ha'dum, strode onto the walkway with Trkider and the others and gave an impromptu speech to unite all the races into a single massive fleet to end the Shadow War forever.
As the war progressed, Trkider was present in the War Room with the other League Ambassadors when they were shown a Shadow planetkiller in action and later witnessed Sheridan ordering Anla'shok Ericsson on a suicide mission to Dorak VII. 
Later that year, Trkider, along with several other League ambassadors became concerned after receiving reports from Drazi pilots that White Stars were sighted on the border of Centauri space engaging in combat, though they could not detect any other ships. Fearing a new hostile species was employing a cloaking system that only the partly Vorlon White Stars could penetrate, Trkider along with Brakiri Ambassador Lethke, insisted that Sheridan put the White Star fleet on their borders, on the pretext that they were owed protection from Raiders after their militaries had been so weakened fighting the Shadows. Unknown to any of them, the whole situation was a smoke screen created by Sheridan to make the League Ambassadors co-operate and forge a stronger interdependency with each other and the Rangers, laying the foundation for what would eventually become the Interstellar Alliance.
In early 2262, Trkider was replaced by Vizak, who returned as Ambassador to B5. Though later that year Trkider would himself also briefly return before again being replaced by Vizak. During his brief second tenure; following suspicions that the Centauri Republic were behind the recent spate of attacks on Alliance shipping lines, Trkider attempted to bug Ambassador Londo Mollari's quarters by having a Drazi cart vendor plant a listening device in a bag of groceries purchased by Vir Cotto. Mollari quickly found and destroyed the bug, though not before mentioning to Vir "conversationally" that Drazi female often prefer to mate with other races rather than males of their own kind and that Trkider's wife had been sleeping with the Gaim Ambassador. Trkider later went to Sheridan, in an attempt to find out if the ISA were hiding what they knew about who was behind the attacks.