After getting a tablet detailing an Ancient treasure trove on Earth, Vala Mal Doran brought the tablet to Dr. Daniel Jackson who translated it, learning that it had been written by the Ancient Merlin. SG-1 was able to track the treasure to Avalon, but when Daniel and Vala used an Ancient long-range communication device, they exposed the existence of human life in the Milky Way to the Ori, Ascended beings that were the Ancients' oldest enemy. Determined to gain more power for themselves and destroy the Ancients once and for all, the Ori started a crusade to convert the Milky Way galaxy to worshipping them, led by the Orici Adria.
Following the beginning of the crusade, the forces of the Milky Way began looking for a way to defeat the Ori. Using Arthur's Mantle, Daniel discovered the existence of a weapon capable of destroying Ascended beings, created by Merlin to combat the Ori. After searching for the weapon for months, SG-1 eventually discovered its location on a planet and undertook a quest to get the weapon, accompanied by Ba'al and Adria. SG-1 eventually located Merlin in stasis and realized that Morgan Le Fay had destroyed the weapon, but left Merlin alive in stasis so he could rebuild it. SG-1 succeeded in convincing Merlin to aid them, but he was too weak to finish the weapon and downloaded his mind into an Ancient Repository of knowledge before dying. After Merlin's death, Daniel downloaded his mind and continued Merlin's work before Adria and her soldiers found them. Daniel killed the soldiers with Merlin's powers and held off Adria long enough for his friends to escape through the Stargate. However, Daniel himself was captured by Adria along with all the knowledge he'd gained from Merlin.
Daniel's plan starts to unfold
After capturing Dr. Daniel Jackson, Adria begins to work on converting Daniel to Origin. Adria confirms what Orlin told SG-1 about the Ori drawing energy from their followers, but claims that its this unselfish act that leads to Ascension and without that power, the Ancients would've destroyed the Ori long before. Adria tells Daniel that the Ancients want the Ori destroyed as they refuse to tolerate anything or anyone that doesn't follow their collective rules, the same reason Daniel was once forced to De-Ascend. Adria further claims that while the Ancients don't interfere, they do manipulate and hoard their knowledge and power to keep anyone below them from reaching their level. Adria is able to get inside Daniel's head with her mental powers, trying to enforce her beliefs upon him and turn him to her way of thinking. As he needed Adria to trust him, Daniel allows her to think that she is turning him when in reality, Merlin's consciousness is able to protect him from her power over his mind and her ability to detect his deception. Eventually Daniel earns Adria's full trust and she uses her pendant to transform him into a Prior, knowing that Daniel is her best shot at converting Earth and Vala.
After being turned into a Prior, Daniel agrees to complete Merlin's weapon for Adria so that she can use it to destroy the Ancients without the Ori having to risk themselves fighting them. Now a Prior, Daniel goes to work on finishing the weapon, building most of it before Adria stops him. Daniel realizes that Adria fears the Ancients will take the weapon away before they can use it and Adria tells him that the Ancients interfered once before in its creation and he is using Merlin's knowledge to build it. She tells Daniel that he must bring the energy of more followers into the fold so that they can build up the Ori's power enough that they can distract the Ancients long enough for Adria to finish the weapon and use it to destroy the Ancients. Daniel finishes building the weapon components before he and Adria set out to convert more followers to Origin.
Capture of Daniel Jackson
As he and Merlin planned, Daniel visits a planet where he learned SG-1 would be visiting in order to preach Origin to the masses and set himself up to be captured by SG-1. SG-1 eventually arrives when Daniel returns to the planet to continue preaching and they decide to capture Daniel in the hopes of turning him back to normal. With the support of General Hank Landry, SG-1 takes the Odyssey to the planet where they beam aboard into a room with an active Prior disruptor and Lieutenant Colonel Cameron Mitchell and Typhuss. To their surprise, Daniel is more annoyed that it took them so long to reach him than anything else and Mitchell stuns him with a zat'nik'tel. The Odyssey then departs for Earth and Daniel is securely restrained on board in a secure room with the Prior disruptor.
When Daniel wakes up, Mitchell informs him that if he tries anything, he will be beamed into space, but Daniel tells them that he's not a threat to them and him becoming a Prior was part of his and Merlin's plan. Daniel tells the team that when they left him behind on the jungle planet, he allowed himself to be captured as he knew the Sangraal was their only chance of destroying the Ori. Daniel explains how after his capture, Adria had begun trying to convert him to Origin and he let her believe she was turning him so that she would trust him. Vala questions Daniel's ability to fool Adria since Vala couldn't and she's a much better liar. In response, Merlin takes control and explains that he was able to protect Daniel from Adria's power. Daniel goes on to explain that he earned Adria's trust to the point that she turned him into a Prior as he was her best chance at converting Earth and Vala and more importantly, at completing the Sangraal. Daniel explains that Adria knew the Sangraal could wipe out the Ancients without the Ori having to enter an all-out war with them. Daniel admits to agreeing to help Adria finish the weapon, but he hasn't finished it yet as he needed all of the elements of his plan to be in place before he does. When the team questions what his plan is, Daniel tells them he needed Adria to turn him into a Prior so he could steal an Ori warship and fly it through the Supergate to the Ori galaxy where he will use it to destroy the Ori. When Colonel Samantha Carter points out that the Supergate is blocked by an incoming wormhole, Daniel reveals he allowed himself to be captured as he needs SG-1 to unblock it.
Returning to the SGC, the team briefs General Landry and General Jack O'Neill on the situation. However, they remain skeptical of Daniel's claims as they want to believe him, but know that if Adria really did manage to brainwash Daniel, the whole thing could be part of an elaborate plan to get them to shut down the Supergate so that the Ori can bring more ships to the Milky Way. In an attempt to find out more, O'Neill visits Daniel on board the Odyssey himself and Daniel reveals that him being a Prior is only temporary. Daniel explains that Merlin knew that Daniel's body could only hold the knowledge and consciousness of two people for so long so he programed in a time limit. When that time limit is up, Daniel's body and mind will revert to the state it was in before Merlin downloaded his consciousness, getting rid of Merlin but Daniel's Prior abilities too. While O'Neill sees that as good news, Daniel tells him that at that point he won't be able to fly an Ori ship and Adria will have Merlin's weapon which is very close to completion. As all the pieces are there, Adria will eventually be able to figure out how to finish and use the weapon. Daniel tells O'Neill that he only has a day or so before he reverts since it took SG-1 longer to capture him than he had planned on. When O'Neill questions that, Daniel explains he couldn't approach them directly without Adria suspecting something was wrong. However, O'Neill remains skeptical that Daniel is telling the truth, especially given how big of a thing he is asking him to do by shutting down the Supergate. O'Neill tells Daniel that even if he does believe him, Carter doesn't think the Supergate can be disconnected. Daniel tells O'Neill that a Mark IX beamed directly behind the Stargate in the Pegasus galaxy will destroy that Stargate and sever the connection. Daniel pleads with O'Neill to trust him, but O'Neill refuses to listen and leaves.
Returning to Earth, O'Neill brings the information Daniel gave him on severing the connection to the Supergate to Carter who is able to confirm that Daniel is right about it. Still not sure if they can trust Daniel, O'Neill sends Typhuss to interrogate him. Typhuss questions Daniel on why he was trying to convert a planet instead of finishing the weapon which would draw Adria's suspicion. Daniel explains that Adria was the one who stopped him before he completed the weapon because she feared that the Ancients would take it away since they interfered before and Daniel is using Merlin's Ascended knowledge to build it. Daniel tells Typhuss that Adria's plan is to gather the energy of more followers into the fold so that the Ori can engage the Ancients and distract them long enough for Adria to finish the weapon. The Ori will then back off while Adria uses the weapon to destroy the Ancients. Typhuss questions why the Ancients don't simply take the weapon now since they perceive it to be such a threat, but Daniel doesn't know, suggesting that maybe the Ancients want to give his plan a chance to work. As the Ori need more followers to build up their power for Adria's plan, Adria is out recruiting more planets to their cause, giving Daniel the perfect chance to use the weapon on the Ori if SG-1 will believe Daniel is still on their side. Daniel earnestly implores Typhuss to trust him as they are running out of time for his plan to work.
Typhuss returns to Earth where he informs the rest of SG-1 and O'Neill that he believes Daniel's story. However, Richard Woolsey has come to the SGC and informs them that he has recommended that Daniel be killed. Afterwards, Vala visits Daniel who is annoyed when Vala tells him that they are on a deadline, thinking that she means until he overcomes the Prior disruptor. Vala tells him that while Typhuss and O'Neill believe him, Woolsey doesn't. Daniel realizes that Woolsey wants to have him killed and explains to Vala about how Woolsey had argued for Khalek to be kept alive and it went badly. Vala confirms that Daniel's right and Daniel realizes that she doesn't believe him. Vala points out that Adria is very dangerous which she knows better than anyone and that by trusting him, they are taking a chance on opening the door for the final Ori victory over them. On Earth, Landry and O'Neill argue with Woolsey about what to do since they don't want Daniel killed while Woolsey does since the Prior disruptor will eventually lose its hold over Daniel and they won't be able to control him anymore if he's a threat to them. Landry tells Woolsey that if Daniel has turned, the Ori have likely already learned all they can from him. Landry reminds Woolsey that Daniel claims he'll revert to normal shortly and they can wait to see if that happens and if it doesn't, they can put him in stasis instead of killing him. Woolsey remains skeptical, but O'Neill points out to him that if Daniel isn't lying, then by not listening to him they are throwing away their best chance of destroying the Ori.
After the argument, O'Neill joins SG-1 in Carter's lab where Mitchell suggests that SG-1 go after the weapon themselves and use it. SG-1 tells O'Neill that Daniel should be able to tell them where the ship is and how to get aboard undetected and Carter figures that Daniel has a good enough understanding of their technology by now to give her what she needs to interface with ship's control systems. O'Neill reluctantly agrees to ask Daniel who finds what SG-1 is suggesting is crazy, believing that he is the only one who should undertake the mission. O'Neill tells Daniel that his plan was a bad one and presses Daniel for the intelligence he needs to complete the mission. At O'Neill's insistence, Daniel finally tells him what he wants to know. Based on Daniel's information, SG-1 later briefs Landry and Woolsey on their plan: the Ori ship is in orbit of a planet with a Stargate and the Prior in charge preaches to the masses on the planet daily. With the Prior distracted, they can reach the planet through the Stargate, board the ship through the rings and hijack it using the information Daniel gave Carter on how to hack the ship's systems. Daniel also gave them instructions on how to complete the weapon and the Daedalus will be standing by in the Pegasus galaxy to shut down the Supergate upon their command. Once the Supergate is shut down, they will use the Ori ship to dial out and send it and the weapon through, but not before the Odyssey beams them out. SG-1 will be able to tell if Daniel is telling the truth before they shut down the Supergate, meaning that the only thing at risk will be them. After hearing what they have in mind, Woolsey reluctantly agrees to their plan.
As SG-1 sets off on their mission, Woolsey visits Daniel on the Odyssey who believes Woolsey is there to execute him and is angered as he gave O'Neill the information they asked for. Woolsey tells Daniel that he is going to be put into stasis and will be allowed to finish transforming back into himself if it turns out he told the truth. Woolsey orders Daniel beamed into the stasis pod in the Antarctic outpost, but Daniel overcomes the Prior disruptor and prevents the Odyssey crew from beaming him out. As Woolsey realizes what's happening, Daniel frees himself, overpowers the guards and locks Woolsey in the room with him. Daniel then hijacks the Odyssey and beams Woolsey and the crew to Earth and beams O'Neill on board. Daniel tells O'Neill that he has hijacked the Odyssey and beamed the crew to safety, but he needs O'Neill's help. Daniel then takes the Odyssey into hyperspace on a course for the Supergate.
Later, as the Odyssey makes its way towards the Supergate, O'Neill questions Daniel on why he'd give him the intelligence if he planned on escaping and completing the mission anyways. Daniel explains that he's now improvising as he had no idea when or if he would've been able to overcome the effects of the Prior disruptor. As Adria would notice his absence soon and start growing suspicious, he saw sending SG-1 to get Merlin's weapon at the time. Daniel tells O'Neill he escaped as he didn't think SG-1 could finish the job without him and he wasn't going to let Woolsey freeze him in stasis, something O'Neill gets.
Fall of the Ori
SG-1 manages to board the Ori warship containing Merlin's weapon through the ring transporter. On the ship, they are engaged by four Ori soldiers who refuse to surrender. SG-1 quickly takes out the soldiers and Vala and Mitchell make their way to the room with the weapon while Carter and Typhuss make their way to the ship's bridge. In the room with the weapon, Vala and Mitchell find all of the components of the weapon seemingly in place and Vala starts putting it all together. At the same time, Typhuss takes out more Ori soldiers he discovers heading towards the bridge, allowing Carter to seal off their level and lock out the rings so they won't be interrupted by enemies. Having gotten control of the ship, Carter takes it to hyperspace on a course for the Supergate. As the ship heads for the Supergate, Vala works on putting the weapon together while Mitchell watches. Finally, when they are nearly at the Supergate, Vala completes putting the weapon together. After its ready, Vala looks around for an Ancient to come and take it and is surprised when no one tries to. Mitchell and Vala speculate that either the Ancients don't mind them using the weapon to destroy the Ori, or Vala put it together wrong and it won't work anyways. Shortly after Vala finishes assembling the weapon, the Ori warship emerges from hyperspace to find another warship waiting for them, guarding the Supergate. As Carter tries to raise the ship's shields, Vala and Mitchell are forced into a standoff with four Ori soldiers while Adria herself captures Carter and Typhuss.
As Adria captures SG-1, the Odyssey arrives nearby and cloaks. Daniel realizes that Adria must've anticipated his plan and planned accordingly. He tells a surprised O'Neill that the Odyssey is now cloaked which he was able to install thanks to the Odyssey now having a ZPM. Daniel tells O'Neill to give the order to the Daedalus to destroy the Stargate in the Pegasus galaxy when the time comes before beaming over to the Ori warship. On the ship, Daniel secretly holds the Prior disruptor behind his back while telling Adria that due to his actions, the Federation are now about to shut down the Supergate so that their ships can come through and they completed the weapon without the Ancients interfering. Daniel tells Adria that thanks to him, they can destroy the Ancients right now and the Ori won't even have to fight and claims to have done everything for her. Adria tries to read his mind to see if he's telling the truth, but finds that his mind is closed to her. Now knowing for sure that the Prior disruptor is blocking Adria's powers, Daniel fires a blast of energy through her personal shield, knocking Adria out. As Typhuss aims his phaser at him, Daniel apologizes for the deception, explaining he needed to be sure the Prior disruptor was affecting Adria's powers first. However, the time limit Merlin installed is nearly up and Daniel used up most of his energy stunning Adria, causing him to collapse into the ship's control chair. Daniel orders Carter and Typhuss to arm the weapon and tells them that O'Neill is on board the Odyssey and will shut down the Supergate for them. As Carter and Typhuss leave, Daniel contacts O'Neill and orders him to shut down the Supergate. After a moment's hesitation, O'Neill contacts the Daedalus and orders them to destroy the Pegasus Stargate.
Racing to the chamber with the weapon, Carter and Typhuss zat the Ori soldiers that are still in a standoff with Mitchell and Vala and inform them of the situation. Carter orders Vala to arm the weapon which she does, adding the crystal that sets a five-minute timer until detonation. As the team rushes through the ship towards the bridge, the Supergate disengages and Daniel dials out to the Ori galaxy. Daniel sets the ship on a course for the Supergate before passing out as Merlin's timer ends. As the rest of SG-1 enter the bridge, Daniel's body reverts to normal and Merlin's consciousness is destroyed. Seeing the Ori warship is fast approaching the Supergate, Carter quickly signals O'Neill who beams SG-1 aboard the Odyssey.
Moments after SG-1 is beamed out, the Ori warship enters the Supergate and travels through it to the Ori galaxy. Once there, the timer reaches its end and Merlin's weapon detonates, killing the Ori.
Sometime later, Daniel awakens in the Odyssey infirmary where the team informs him that they successfully armed the weapon and sent it through the Supergate. Daniel tells them that Merlin is gone, having sacrificed himself to destroy the Ori. Vala tells him that Adria was still on the Ori warship when it went through the Supergate and Mitchell wonders how they will know if it worked. Daniel admits that they have no way of knowing yet and Vala speculates that the Ancients allowed them to enact Daniel's plan as they knew it wouldn't work. Daniel counters that the Ancients may have known it would work and wanted it to so they allowed it, but feels there's no point in guessing. Teal'c reminds them that even if the Ori are dead, the fight isn't over yet as there are still many Priors with armies of warriors bent on converting the galaxy who it will be hard to convince that their gods are dead. Mitchell informs Carter of Daniel being awake and she quickly summons them to the bridge as she notices the Supergate reactivating with an incoming wormhole. As they watch from the Odyssey bridge, six more Ori warships arrive through the Supergate to join the one still waiting there. The seven Ori warships then jump to hyperspace to continue their conquest of the Milky Way Galaxy. Mitchell and Daniel point out that they knew that killing the Ori might not stop their followers, but it was still the right thing to do. Mitchell tells the others that they may have made things worse at the moment by reopening the Supergate to the Ori followers with their mission, but that it might be their only chance to win the war in the long run.
Although SG-1 managed to deploy Merlin's weapon, they remain unaware of the fate of the Ori for some time. Adria later claims that the Ori were not destroyed while a Ba'al clone using Adria as a host tells them that the Ori were in fact destroyed. While later hunting for the Ark of Truth to brainwash the Ori followers into believing the truth, Hertis tells them that the fires of Celestis have gone out. As the Ori manifest as those fires, they take it as further proof that the Ori are dead. Eventually they learn from an Ascended Adria that the mission was successful and the Ori were destroyed by Merlin's weapon.