- "I can't think of a better first operational mission for the Odyssey than to bring home SG-1."
- ―Colonel Paul Emerson[src]
Emerson led the Odyssey, participating in various missions up until his own murder at the hands of the Lucian Alliance during the Hijack of the Odyssey.
Captain of the Odyssey
Emerson's first mission with the Odyssey was to rescue SG-1 from P6G-452, which he pointed out to be a great first mission. He then commanded the Odyssey in the battle with Ba'al's Ha'tak. When the Ha'tak was destroyed, he believed SG-1 was killed but they had escaped through the Stargate. (SG1: "Off the Grid")
Battle of P3Y-229
Later, he traveled to Camelot and picked up SG-1 to take them to the site of the newly formed Supergate. Once there, Lt. Colonel Samantha Carter and Kvasir attempted to dial out but the Ori dialed in first. He then commanded the Odyssey in the Battle of P3Y-229. He and his crew were fortunate to survive the massive Ori invasion, as his ship was one of only two out of a dozen ships to survive the battle. After the battle, he retrieved Lt. Colonel Cameron Mitchell from his F-302 fighter-interceptor. Mitchell then piloted the Odyssey to pick up Carter, who was floating in space. He also beamed several people from other disabled ships to the Odyssey but was nearing the limits of its life support systems. After getting the hyperdrive online, he headed to Chulak to check on SG-1. He was able to beam SG-1, Bra'tac and Vala Mal Doran aboard and escape into hyperspace. (SG1: "Camelot", "Flesh and Blood")
Traveling to the Pegasus Galaxy
He flew the Odyssey on its mission to the Pegasus Galaxy and the effort to neutralize the Ori Supergate. He dropped off supplies to Atlantis and headed to the black hole. After the first two attempts to make the Stargate jump failed, he was concerned about bringing the Odyssey closer to the black hole but was convinced by Colonel Carter that it was worth the risk. When the ship came under attack by a Wraith Hive Ship which had presumably arrived to investigate the explosions, he ordered a slingshot maneuver around a black hole in order to gain them tactical advantage. When the Hive flew next to the Gate, Carter beamed the Nuclear warheads aboard the Hive and destroyed the ship. (SG1: "The Pegasus Project")
Dealing with the Dakara Superweapon
He joined SG-1 on a mission to a planet that had fallen to the Ori. When Major Kevin Marks detected an energy wave coming from the Stargate, he ordered him to beam them aboard. He sent Lt. Evans to investigate and they discovered the energy was from the Dakara superweapon and it had completely destroyed all organic matter. They then beamed SG-1 to the unmanned Ori warship. When the ship took off from the planet and entered hyperspace, he correctly assumed it was headed for Dakara and ordered Major Marks to plot a course for Dakara. He was then able to beam them off the Ori ship before it was hit by the Dakara superweapon and escaped into hyperspace. (SG1: "Counterstrike")
Captured by the Lucian Alliance
When the Lucian Alliance attacked the Odyssey and boarded it, their leader Anateo summoned Colonels Carter and Emerson to the bridge so that Carter could repair the ship. Emerson ordered her not to cooperate, making it an order. In response, Solek, one of Anateo's associates shot Emerson in the heart, killing Emerson instantly before proceeding to fire two more shots into Emerson's body as Carter looked on, horrified. (SG1: "Company of Thieves")
- Is the second commander of an Earth-based ship to have been killed in the line of duty, the first being Colonel Lionel Pendergast who died during the Battle of Tegalus which occurred in the Stargate SG-1 Season 9 episode, Ethon.