Sheridan agreed to travel to Z'ha'dum with Anna to hear out the Shadows' representatives on a way to stop the war, despite Kosh's warning that he would die there. All of Sheridan's crew on Babylon 5 tried to convince him it was a bad idea, but he went anyway. They traveled to Z'ha'dum. aboard the White Star 1, taking no other crew on the ship. Unknown to all but Garibaldi, he smuggled two thermonuclear devices aboard, their detonators connected to his link.
On the Shadow homeworld, Sheridan met with the leader of the Shadows' human thralls, Justin, who gave him a long explanation of what made the Shadows and Vorlons different, in an effort to get Sheridan to back down from the war and allow the League worlds to continue fighting. Despite his diplomatic behavior, Sheridan never had any intention of acquiescing to the Shadows, and they attacked him. Though his primary sidearm had been taken by Morden, Sheridan pulled a hold-out weapon and fought out of the facility.
When he had no chance of escape, Sheridan contacted the White Star remotely and ordered the ship to come crashing into the city. Just as the ship headed through the atmosphere, the soulless form of his wife approaching from behind him, Sheridan heard a voice in his head, telling him to "jump". He dove into a deep crevasse in the planet, just as the nukes detonated overhead, obliterating the Shadow city. The explosion obliterated the capital, leaving only a smoldering crater behind.
John Sheridan rediscovered Lorien on Z'ha'dum, deep inside the pit he jumped into on the orders of Kosh. Sheridan had actually died from the fall, but Lorien was able to resuscitate him for a time. Lorien then gave him some of his own life force to sustain Sheridan, but only for 20 years. Together, they boarded a ship and returned to Babylon 5, where Sheridan reunited the rapidly-deteriorating forces of the League in preparation for the next phase of the war, when the younger races would free themselves from the influences of both the Shadows and the Vorlons.