- "Well, that was refreshing! He didn't try to kill us even once!"
- ―Rodney Mckay
When Cowen was first encountered by Major John Sheppard's team, they believed he was the leader of a simple Amish-like people. They began to negotiate for a piece of their Tava bean crop. He was hesitant at first because he said it would require them to clear land. Sheppard then showed them an easy way to clear a stump using C-4. He agreed to give them a supply of Tava in exchange for some C-4 and medical supplies. After getting clearance from Dr. Elizabeth Weir, Sheppard returned by Dr. Rodney McKay detected traces of radiation and followed it to a hatch to an underground bunker. They were detained by military personnel and then Cowen entered the room in uniform. He explained the Genii used to be a Confederation of planets but know hide underground from the Wraith. McKay realizes the radiation is from the development of Nuclear warheads. Sheppard offers their help in there creation if they form an alliance against the Wraith. Cowen wants to use a Puddle Jumper to infiltrate a Hive Ship and access data core. Sheppard agrees and they head for the Hive. Once there, they get the info but Tyrus is shot with a Wraith stunner and left behind. Once back on the Genii homeworld, Cowen's men surround the team and blame Teyla Emmagan for his death. Sheppard then orders two Jumpers to decloak and Cowen stands down. (SGA: "Underground")
After learning that most of the personnel on Atlantis were being evacuated by Smeadon, he ordered Commander Acastus Kolya and his team to invade it and retrieve the Wraith data storage device. (SGA: "The Storm")
When Ladon Radim came to the Atlantis expedition for help in overthrowing him, Lt. Colonel John Sheppard and Dr. Rodney McKay came to warn him. He appeared grateful for the information. When Sheppard and McKay decided to squash the coup themselves, they were knocked unconscious by gas. When they awoke, Cowen was there to greet them and told them he knew of the coup the entire time and that Ladon had the best interests of the Genii at heart. He then contacted Dr. Elizabeth Weir and demanded all of their Puddle Jumpers in exchange for their lives. Unknown to him, Ladon was planning a coup and planted a Genii nuclear bomb in the building. He along with his personal guard were killed in the blast. (SGA: "Coup D'etat")
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