"That's what makes this war different than anything we've ever fought before: this time we know everyone we kill."
- – Major Ryan
In the summer of 2259 General Hague introduced Major Ryan to the Captain of the EAS Clarkstown, a friend of Hague's from his Academy days. Ryan got to know the Captain, learning of wife back home on Earth, his three small children and his Abyssinian cat named Max.
In 2260, Major Ryan was serving as the second in command of Hague's flagship, the destroyer EAS Alexander. Following EA President Clark's martial law decree and dissolution of the Earth Senate, Ryan remained loyal to Hague and assisting him in an attempted coup that ultimately failed.
Ryan was forced to assume command of the Alexander when General Hague was killed when the EAS Clarkstown ambushed them while returning from a meeting with some officials on Orion VII. Reluctantly, and at the urging of acting XO Bill Trainor, Ryan ordered the Alexander to destroy the Clarkstown. Needing to repair the ship and plan their next move, Ryan ordered the ship taken to Babylon 5, knowing Captain John Sheridan had been a close ally of Hague. He sends a message ahead so that just as he arrives the station can cut all outgoing communication channels.
Once aboard, he informs Sheridan and his staff about the death of Hague and the status of Earth—elite shock troops are out everywhere. Ryan is hopeful that Mars, which has rejected the martial law order, can form a coalition against Clark. However, during the meeting news comes in that Clark has ordered the bombing of civilian targets on Mars. Before going off the air, ISN reports that Orion VII and Proxima III have declared independence in response. Meanwhile, the EAS Churchill under the command of Captain Sandra Hiroshi jumps into B5 space. Hiroshi, an ally of Ryan's, informs him and Sheridan that Clark has ordered a fleet to seize Babylon 5, arrest the senior staff, and place it under his direct control. Ryan offers to leave and perhaps draw off some of the enemy fire, but Sheridan insists they make a stand together. Just before Clark's task force arrives, Sheridan announces that Babylon 5 is declaring independence from the Earth Alliance until Clark is removed from office.
The task force soon arrives, and when Sheridan rejects their call to surrender, the Battle For B5 Independence begins. Ryan commands the Alexander with Bill Trainor as his second-in-command. The battle ends in a victory for the rebels, but at a high cost. Ryan decides to take his ship out after it finishes repairs, diverting the attention away from the station. He plans to track down any other defecting ships and bring them together to hopefully end the Civil War.