Under the command of a Wraith Commander, Ember travels to M4F-788 and uses Wraith modification equipment to enable the planet's Stargate to dial the McKay/Carter Intergalactic Gate Bridge and Midway Station. When the Stargate activates due to Ronon Dex and Teal'c traveling to Midway, Ember notes the travel to his commander. Finally, Ember is able to enable the Wraith to dial Midway and he joins the attack force that travels through the Stargate.
On Midway, Ember works on the computer systems in order to allow the Wraith to dial Earth, but finds that Doctor Bill Lee has placed a lockout command within the systems. As Ember's commander attempts to force the humans to give up the command code, Ember finally breaks into the systems and dials Earth, allowing the Wraith to send through a bomb and then an invasion force. Ember continues to monitor the systems in the control room, placing a lockout in the Stargate control system when a Tau'ri strike force arrives led by Lt. Colonel John Sheppard. Though his commander abandons the control room when the Tau'ri attacks, Ember remains inside. After Sheppard kills the Wraith warriors guarding the control room, Ember makes a grab for one of the warrior's Wraith spear gun only to have Sheppard shoot him three times with his Colt M1911A1 pistol, apparently killing Ember. (SGA: "Midway")
Despite being shot by Sheppard, Ember survives his wounds and apparently plays dead. After the humans evacuate, Ember is presumably able to use the Stargate to escape before Midway is destroyed. He rejoins his hive ship before it is eventually destroyed and then joins the crew of Just Fortune. (SGA: "Legacy: Homecoming")
Six months after the Battle of the Super-hive, Guide returns to Just Fortune where Bonewhite introduces him to Ember who is attempting to repair a dangerous hull breach that is giving the crew trouble. Ember, as Just Fortune's Master of Sciences Biological, joins Guide's party to meet Queen Death where he is swayed by her beauty along with most of the Wraith present. As part of a ritual greeting, Queen Death feeds from Ember briefly before allowing the Wraith from Guide's party to feed themselves. Though Guide considers protesting Queen Death's actions, he knows that if he does, he risks her killing Ember and he can't afford that. (SGA: "Legacy: Homecoming")
During the Second Battle of Atlantis, General Jack O'Neill contacts the Wraith and asks for help in dealing with a Wraith cruiser heavily rigged with explosives. Ember volunteers to help and travels to the cruiser on a Wraith Dart where he helps Teyla Emmagan gain control of the ship and move it away from Atlantis. Ember then works with Doctor Radek Zelenka to disarm the bombs completely and remains on the cruiser with Zelenka and Doctor Eva Robinson when Teyla leads a boarding party from the cruiser to Queen Death's hive ship. Ember, aided by Zelenka, uses the cruiser to drain power from Queen Death's hive ship in order to even the odds, but in doing so, draws the wrath of two more cruisers. As the two flee to a Puddle Jumper, Ember shields Zelenka from an explosion, saving Zelenka's life, but suffering mortal wounds himself in the process. Knowing that Ember needs to feed to survive, Zelenka, who has taken a new retrovirus, allows Ember to feed on him. Due to the new retrovirus, Zelenka survives unharmed and Ember is able to heal his own injuries.
Following the battle, Ember chats with Zelenka about the behavior of Doctor Rodney McKay when he was both Wraith and human and the two commiserate over their respective experiences with McKay. Ember tells Zelenka that what Zelenka did, giving Ember some of his own life to save Ember's is the mark of brothers and if Zelenka is willing, he is willing to hold Zelenka as such. While stunned by the offer, Zelenka tells Ember that he is honored to be his brother and accepts. Ember then departs on the Eternal with Guide and the other Wraith. (SGA: "Inheritors")
When Atlantis is infected by a plastic-eating disease, Ember offers his help as Master of Sciences Biological. Ember recognizes what they are dealing with as alflageolis, a biological Wraith cleaning solvent, but is confused by its behavior, especially after his attempts to shut it down fails. Examining the alflageolis, Ember is horrified to discover a bacteriophage he recognizes as The Little Replicator as having infected the alflageolis. Ember works alongside the Atlantis expedition scientists in an attempt to find a way to destroy the mutated alflageolis. Eventually, Ember comes up with a bacteriophage of his own that when released throughout the city, destroys the infected alflageolis.