Cowen led the Atlantis Away Team to believe that all Genii were an Amish like people. He was hesitant to trade food with them, but changed his mind after seeing C-4 clear away a tree stump. After Sheppard clears it with Dr. Weir they return to the Genii Homeworld with C4 and medical supplies.
Dr. McKay detects a weak radiation signal and follows it to a hatch that leads to an underground bunker. After they’re detained by a heavily armed Genii military team Cowen enters the room dressed as a high ranking Genii military officer.
He explains that the Genii hide underground from the Wraith. As long as they don’t know they’ve developed and grown as a people they are mostly left alone. The food they grow above ground is only just enough for the people living underground. They want to fight the Wraith and are in the process of building a nuclear bomb. But many scientists are killed by the radiation poisoning. John Sheppard offers to help them infiltrate a Hive Ship with a Puddle jumper and Dr. Rodney McKay helps them perfect the nuclear bomb.
After the mission, where they lose one Genii called Tyrus, Cowan turns against the Atlantis team and surrounds them in order to take their weapons and the puddle jumper. Unfortunately for him John Sheppard expected this move and decloacks two puddle jumpers after which Cowen stands down.
He later ordered Commander Acastus Kolya to invade Atlantis during a storm to retrieve the Wraith data storage device they stole during the first expedition and a load of C-4. Kolya eventually loses and returns to the Genii home world.
Cowan is later overthrown as Genii leader by Ladon Radim who plans and executes a coup against him. Cowen dies in the blast of a Genii A-bomb.