"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 assisted him in an attempted coup that ultimately failed.
Ryan was forced to assume command of the Alexander when General Hague was killed when the 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 his vessel and plan their next move, Ryan brought the ship to Babylon 5, knowing Captain John Sheridan had been a close ally of Hague. He sent a message ahead so that just as he arrived the station could cut all outgoing communication channels.
Once aboard, he informed Sheridan and his staff about the death of Hague and the status of Earth — elite shock troops were out everywhere. Ryan was hopeful that Mars, which had rejected the martial law order, could form a coalition against Clark. However, during the meeting news came that Clark had ordered the bombing of civilian targets on Mars. Before being violently taken off the air, ISN reported that Orion VII and Proxima III had declared independence in response. Meanwhile, the EAS Churchill under the command of Captain Sandra Hiroshi jumped into B5 space. Hiroshi, an ally of Ryan, informed him and Sheridan that Clark had ordered a fleet to seize Babylon 5, arrest the senior staff, and place it under his direct control. Ryan offered to leave and perhaps draw off some of the enemy fire, but Sheridan insisted they make a stand together. Just before Clark's task force arrived, Sheridan announced that Babylon 5 would declare independence from the Earth Alliance until Clark is removed from office.
The task force soon arrived, and when Sheridan rejected their demand for surrender, the Battle For B5 Independence began. Ryan commanded the Alexander with Bill Trainor as his second-in-command. The battle ended in a victory for the rebels, but at a high cost. Ryan decided to take his ship out after it finished repairs, diverting some attention away from the station. He planned to track down any other defecting ships and bring them together to hopefully end the Civil War.