As the Ruler of Theramore, Jaina led the town and was found in her tower. Having partnered with the Stormwind kingdom, she insisted on making a summit between Thrall and King Varian Wrynn. Varian was convinced by his son Anduin but during a journey by the sea, Varian mysteriously vanished.When an investigation about the missing King Wrynn and the Defias Brotherhood was going on, she and Tervosh helped to capture Hendel who was allied with the Defias Brotherhood. Around the time of Zul'jin's fall, Jaina was able to discover that the Defias Brotherhood who kidnapped Varian was allied with Onyxia. She immediately sent this information to Bolvar. (As of 4.0.3, she informs Varian, who no doubt would want to make an example out of the rest of them, of the connection between Defias and Onyxia.)
After Onyxia was killed, Jaina was also the primary instigator in proposing an alliance between the humans of Stormwind and the orcs of Orgrimmar on the way back to Theramore. Varian was convinced and she traveled to Razor Hill where she met with Thrall and told him the story of Varian. The orc leader also agreed to the meeting, despite having reservations since Orgrimmar sentiment was becoming increasingly restless with the arrival of Garrosh Hellscream. Jaina then returned to Theramore, where she prepared for the peace summit, and ultimately welcomed Thrall and his advisers: Rehgar and Garrosh. Although the conference had a promising start, it was ambushed by Twilight Hammer cultists comprising of races from both the Alliance and the Horde. The attack sowed distrust between the human and orc delegates who had suspicions that the opposite faction may have lured them into a trap. Ultimately, the attempted assassinations on the human and orc leaders effectively ruined any chance of a human-orc alliance. One of the Twilight Hammer assassins was Garona Halforcen, who was left for dead or to be captured by her fellow assassins. Before King Varian could kill her, Lady Jaina claimed Garona as her prisoner with the intention of interrogating her. King Varian allowed it, so long as she shared the information with his adviser, Valeera Sanguinar, who will be conducting the investigation on identifying the perpetrators. However, King Varian also claimed he will return to claim Garona for execution. Jaina and Aegwynn discovered that there was a spell placed on Garona's mind but could not remove it without causing her great pain and possible death. In a deal Garona made with Valeera Sanguinar, Garona agreed she would endure the pain and give them some of the information they required if Valeera used the information to go save her son Med'an from the Twilight Hammer cult.
Suddenly, the Lich King entered the chambers and Uther was sucked back into Frostmourne. The Lich King coldly acknowledged Jaina while removing Frostmourne from its pedestal. The Lich King summoned Falric and Marwyn, two captains Jaina fought alongside during the Third War. As The Lich King retreated to his private chambers and sicked the captains on her allies, Jaina remained determined to save Arthas and pursued him as the doors behind her closed. Following the defeat of the two captains, Jaina's allies rushed to her aid only to find her on the verge of defeat, with her former love viciously attacking her. Heartbroken and realizing that there was truly nothing left of Arthas, Jaina and her allies fled down the Hidden Passage with the Lich King in steady pursuit. As they came to a cliff, the Skybreaker flew in and rescued them at the last moment.
Following the battle at Lordaeron, the Horde infiltrated Stormwind and freed two Zandalari prisoners: Princess Talanji and Zul. Jaina confronted the Horde forces at Stormwind Harbor, but a fire started by Zul forced her to put it out and save the city instead of capturing them. When only one of the eight warships that pursued them returned, Jaina used her magic to view a survivor's memories and learn that the Horde had allied with the Zandalari. In response, Jaina suggested to Anduin that she should travel to her homeland of Kul Tiras and recruit its legendary fleet. While Greymane reminded Jaina that she was the reason Kul Tiras left the Alliance in the first place, Jaina insisted that dealing with that was the only hope they had of bringing them back. She promised to return with the fleet or not at all.
At the memorials to Daelin and Derek, Jaina, Tandred, and Katherine spoke about how Jaina had always expected Derek to be Lord Admiral, how Derek's corpse had been retrieved from the ocean floor by the Horde and used to taunt the Proudmoores, and what Derek and Daelin would think of all that their family and Kul Tiras had endured. Suddenly Taelia Fordragon arrived with a report that the Horde was attacking Anglepoint Wharf, and Jaina left to confront the Horde personally while Katherine and Tandred rallied defenses. On the boat ride to Anglepoint, Jaina reassured Taelia that though she had not wanted to leave her team to report the attack, it was the right thing to do. Jaina assured her that even in times when they cannot save everyone, they should do the best they can and never give up hope. At Anglepoint Jaina teleported civilians out, then had Taelia and the Alliance champion work with the Outriggers but left behind one of her water elementals to help. Jaina later froze the seagate's water to prevent the Horde from entering Tiragarde Sound, and teleported the team atop the walls. Using Azerite bombs stolen from the Horde, Jaina destroyed the invading ships.
In Nazmir, the Alliance began a feint attack led by Blademaster Telaamon to bait the Horde out of Zuldazar while the Alliance prepared to attack Dazar'alor. They would cover the area in a mist with the Abyssal Scepter, and until it was set up Jaina and Shaw provided support for Telaamon's forces. Afterward the two of them led the Alliance forces to get as much of Nazmir as they could, to make the Horde think it was where their main fleet was. Alongside the adventurer, Jaina marched into Zuldazar aboard controlled Zandalari direhorns from the northern border to take the Blood Gate, clearing the way for Alliance forces. Before returning to Boralus, she bid farewell to Telaamon and promised his sacrifice would be remembered. Jaina and her ship spearheaded the Alliance navy's assault on Dazar'alor. Once they were within range, the Alliance planned to detonate the hidden explosives they planted on the Golden Fleet's ships. The Golden Fleet, however, began harrying the Alliance navy with their ballistaes and one of them collapsed the deck by Gelbin Mekkatorque's position just as he was about to detonate the explosives. Jaina began using her magic to shield her ship from missiles; just long enough for Mekkatorque to re-position his remote detonator machine and blow up the entire Golden Fleet defending the Port of Zandalar. With the Golden Fleet in ruins, the Alliance navy invaded Dazar'alor with little resistance.
After Alliance spies caught wind of Sylvanas Windrunner planning to assassinate Baine Bloodhoof Jaina, recognizing that she owed Baine for returning Derek to her, agreed to Anduin's request to rescue Baine. Thus, she, along with Mathias Shaw and the champion headed off to Orgrimmar. As Jaina and her allies ventured into the Underhold, they unexpectedly encountered Thrall and Varok Saurfang, who had also come to rescue Baine, and after a brief moment, agreed to work together to save Baine. When things started getting heated between Saurfang and Shaw, Jaina and Thrall were quick to get them focused on the task at hand. Upon nearly reaching Baine, the group was attacked by Rowa Bloodstrike, who expressed disappointment but not surprise by Saurfang's and Thrall's decision to rescue Baine. Unwilling to stand down, the group was forced to kill Rowa and moved forward to Baine, who was surprised by their presence. While Shaw moved to release Baine from his chains, Saurfang remarked that it felt too easy and the group was then attacked by Magister Hathorel, who sought to kill them and Jaina in particular for vengeance for the purge of Dalaran. Ultimately, the group was successful in liberating Baine from his chains, and Jaina teleported the group safely out of Orgrimmar into Mulgore.
When the covenants rallied together to defend Ardenweald from the Mawsworn, Jaina and Bolvar joined them hoping to have the chance to save Anduin. During the battle, Jaina blasted an untold number of Mawsworn Realmbreakers out of the skies near the Glitterfall Basin. However, as the battle continued, Jaina grew concerned at Anduin's absence. This concern was warranted as it was revealed that while the Mawsworn did battle with the defenders, the dominated Anduin was sent to acquire the Winter Queen's sigil from the Heart of the Forest, with Jaina and Bolvar arriving to late to stop them and unable to break Zovaal's hold as he carried out the task. Despite this set back, Jaina was undeterred and vowed to save Anduin, no matter what it took.
Sometime later, Jaina and her allies stormed into the Sanctum of Domination in order to stop the Jailer, once and for all. However, despite defeating the likes of The Nine and Kel'Thuzad, Sylvanas was able to stall them long enough for the Jailer to absorb the essence of the Arbiter into his being. Jaina was then briefly controlled by Zovaal through the use of Domination magic before she was released after Sylvanas, who realized that the Jailer never intended to not break the system of Death and give everyone free will as she had believed, but to forge a new reality where all would be forced to serve him, attacked him. In response, Zovaal reunited Sylvanas with the missing fragment of her soul before leaving with the mind-controlled Anduin, and thus allowing Jaina and her allies to imprison Sylvanas.
Jaina briefly appeared on alternate Draenor, helping Khadgar empower the Horde adventurer's legendary ring, but expressed hostility towards the Horde, reminding Khadgar that she and the Council did not want them near their bases, but Khadgar dismissed her concerns. After helping the Alliance fight at the Broken Shore and witnessing Varian Wrynn's death, apparently because Sylvanas and the Horde retreated, she and Khadgar clashed again after he called a Council meeting in Dalaran when she repositioned it over Karazhan to defend the Eastern Kingdoms. This time, Jaina left the Kirin Tor and their city after she was outvoted by most of her peers into allowing the Horde back into the order, calling the Horde monsters and cowards and warning the others that they would eventually betray them again, and subsequently left to fight the Legion by herself. During their last meeting, Jaina told Kalecgos that she still refused to agree with the Council's reasoning and no longer belonged in Dalaran, but that everything she did since Theramore's destruction was a reaction against something, and that she wanted to find out what she truly stood for, in order to find peace. After Kalecgos told Jaina that her true nature would not be anything ugly or cruel, and that he had faith that she would eventually find her way, Jaina replied wryly that he might be the only person in the world who did. 1e1e36bf2d