He fought against Phoebus until they were the last two fighters to the extent that he was able to learn her strengths and weaknesses. When his ship was damaged, he was forced to eject and he survived in a stasis pod in the Kohal system long into old age.
He was retrieved by Lt. Colonel John Sheppard's team in a Puddle Jumper and taken to Atlantis. His consciousness, stored in the headrest of the pod, downloaded itself into a willing Sheppard -- who believed that that would allow Thalan to say goodbye to his wife Phoebus, in the body of Dr. Elizabeth Weir.
Thalan played along with Phoebus's lie until the first opportunity arose to arm himself and fire on his "wife," his blood enemy. He pursued her in Atlantis in hopes of annihilating her for the final vindication of his race. When Sheppard/Thalan were stunned by Teyla Emmagan, Weir/Phoebus ordered that Teyla kill him, lest she pump Halon gas into the Atlantis living quarters. But before Teyla was forced to decide Dr. Rodney McKay overrode Weir/Phoebus's controls, cutting her out of the system.
When Phoebus had Teyla and Sheppard/Thalan cornered, Teyla armed him with a Wraith handblaster, knowing he would have shot Weir either way. He seemed to disappear right before, but its unclear if he was faking. Ultimately either he or Sheppard stunned Phoebus and Sheppard/Thalen was taken into custody until it could be sure he was gone. The last remnants of Thalan soon vanished from Sheppard's conscious mind. (SGA: "The Long Goodbye")
Much like Phoebus, Thalan is also consumed with a very strong urge to kill his sworn enemy. He is also unforgiving which is shown when he brutally knocks two Marines unconscious and also stuns Teyla Emmagan with Ronon Dex's Particle magnum. He is very manipulative as he cons Ronon into thinking that he is actually Sheppard but then leaves him for dead after Ronon is shot by Phoebus although Thalan calls for a medical team, suggesting he might have some degree of mercy or was being influenced by Sheppard. Thalan is also skilled in hand-to-hand combat and heavy weaponry. (SGA: "The Long Goodbye")