"Forces of Order" Campaign
In the Forces of Order campaign, one plays as the Imperial Guard (with occasional allied assistance from the Space Marines) and the Eldar. General Sturnn and the Cadian 412th land on Lorn V, intending to assist the Ultramarines already on Lorn V get a Titan crew to the Imperator Class Titan Dominatus, a massive and powerful humanoid battle machine that can almost win a war by itself. Built in ancient times, the construction of a titan is an enormous undertaking, and any Titans now found are treasured relics. Though the Guard hits a wall (literally) trying to get past the forces of Chaos, the Eldar secretly assist the Guard and disable the gate preventing their progress. Eventually the Guard rescues the Ultramarines and Titan crew, and begins the long trek to the crashed Titan.
The Eldar, led by Farseer Taldeer, do everything in their power to make sure their presence is unknown, but when an Ork with unique technology capable of sensing their teleportation appears, they are forced to reveal their presence, destroy the Ork, and teleport away. Too badly damaged to accomplish their original goals, Taldeer is forced to ask Sturnn for assistance. Sturnn agrees, and the Orks are pushed back.
In the aftermath, Taldeer reveals that she does not care about the Titan, but instead her goal is the Necrons underneath the planet's surface. Ages ago, an ancient race known as the Necrons went to sleep for thousands of years, and now they are awaking. She cannot allow the Necrons to get off Lorn V, because if they do, they will cause untold damage to the surrounding systems before being stopped. The two factions ally, but both know their goals are mutually exclusive. At this point the player may choose to pursue the goals of either the Eldar or the Imperial Guard.
Imperial Guard branch
If the player chooses the Imperial Guard, Sturnn assists the Ultramarines in getting the Titan crew past an alliance of Orks and Chaos into the safety of a waiting psychic shield, preventing their enemies from following them directly to the Titan. However, Taldeer and her Eldar are trapped with the Orks and Chaos, and she tells Sturnn behind the shield that he cannot defeat the Necrons without her. As he will not risk his men for hers, Sturnn and the 412th march on to their goal, while the Eldar are butchered a mere few feet away from them.
Upon reaching the Titan, the Ork/Chaos alliance descends on the Imperial encampment protecting the Titan. The crew begins to work, but they require a massive amount of power to use the Titan, and Sturnn is forced to protect the Titan, several power generators, and a nearby Imperial encampment of survivors from the Forces of Disorder. Although the Titan is too badly damaged to move until extensive repairs can be carried out, its now-operational weapons easily dispatch the Orks and Chaos. However, the Necrons now awaken, and butcher the remaining Ork/Chaos alliance. Beginning their slow march to destroy the only living souls left, the Imperials, they nearly succeed before the Titan Crew is able to destroy the Necron Monoliths using the Titan's weapons. Ultimately, the Cadian 412th and the Ultramarines are successful in repairing the Titan, destroying the Ork/Chaos alliance, and stopping the Necrons before they escaped the planet, but at the cost of Taldeer and her Eldar (which does not bother Sturnn or the Ultramarines in any way).
Taldeer uses Imperial distraction of the Guard and Ultramarines to teleport her buildings, troops, and Soul Stone past the psychic shield. The Ultramarines are slaughtered, but Sturnn and much of the Imperial Guard manage to escape the horde of Orks and Chaos.
Unlike the Imperial Guard campaign, Taldeer does not fight the Forces of Disorder when she reaches the Titan: the Imperial Guard has surrounded her, but the Necrons awake and begin trying to kill the Eldar. Taldeer uses the Soul Stone she sneaked past the shield to utterly destroy a Monolith, but too many more appear before the Soul Stone can recharge. Desperate for a weapon to use, she decides to power up the "primitive, but still powerful" weapons of the Titan surrounding her (able to jury-rig a solution, since she does not have a Titan crew), convinces Sturnn that he can have the Titan once the Necrons are defeated (thus once again gaining the humans as allies), and uses the Titan's weaponry to utterly defeat the Necrons. Although successful in destroying the Necrons of Lorn V and gaining a momentary victory over her undead foes, Taldeer's unfamiliarity with the Titan's weapons systems causes them to explode, destroying the Titan. She and her base manage to teleport away in time, but the fate of Sturnn and his men is left unknown.
Campaign of Disorder
The Campaign of Disorder begins with Warlord Gorgutz trying to unite the Ork Boyz under his control. With Gorgutz's starting force, he launches attacks across Headcrushaz, Rokkitranza, Burnaboyz, and Kwikmeks, destroying their "Big Banners" and uniting them under his rule. His force is eventually stopped by the shielded gate of Footstompaz, which he promptly destroys the generators feeding power to the gate. He soon discovers that Squiggoths are loose in Footstompaz's base. After freeing the Mad Dok from the holding pen, he brings Squiggoths and Footstompaz under his control, after which he attacks a remote Chaos outpost.
Gorgutz, to take his WAAAGH! across the planet, flies to some unknown destination but he is shot down by a Forces of Chaos battery. Gorgutz survives, and the Chaos Lord Crull is out to get him. Crull soons meets Gorgutz's remaining boyz launching assaults on his Temples of Khorne. While trying to kill Gorgutz, Crull realizes Gorgutz is surrounded by a shield, making him invulnerable. Crull soon sets out to destroy the Ork base nearby and also a power generator feeding power to the shield. After destroying Ork's base and the generator, Gorgutz launches a massive assault on Chaos, but Crull promptly returns and puts an end to Gorgutz. Gorgutz is dead, but before Crull can savour his victory the Imperial artillery barrage begins on the location. Gorgutz suddenly springs up, as it turned out he was just playing dead. Crull expects Gorgutz's force to aid him defeating the Imperials, but Gorgutz flatly refuses and escapes to rouse his boyz and kill the "humiez" himself.
Although the game has several endings there is a canonical ending to the game, as established by its sequel Dark Crusade.
- Farseer Taldeer is still alive, suggesting that she might have been the only Eldar that survived the attack from the Chaos/Ork alliance at Mission 4, base on the Dawn of War novels.
- Warboss Gorgutz lives to fight another day, literally. He can be seen in Dark Crusade, leading the Orks again.
- The chaos lord Crull's skull was taken by Gorgutz and can be retrieved in Dark Crusade, given to Eliphas the Inheritor should he be successful in the campaign.
- Should the Eldar defeat the Imperial Guard in Dark Crusade, the narrator states that Farseer Taldeer was branded "an enemy of the Imperium" after her manipulation of the Cadian 412th regiment on Lorn V. Lucas Alexander's regiment was ordered to pursue the Eldar and that "this long chase was finally over" when they faced off at Victory Bay.
- Conversely, if Governor-Militant Lucas Alexander defeats the Eldar in Dark Crusade, the narrator states that his "original mission was at an end", suggesting that his original primary mission was to hunt down Farseer Taldeer for her treachery on Lorn V. His new mission of Liberating Kronus was only given after discovering the Hellstorm Cannon at Victory Bay.
It is thus likely that the canonical ending is the not just one ending but two: the Eldar/Ork ending: Taldeer escapes from Lorn V to continue her mission to stymie the awakening Necrons, much to the surprise of the Imperial Guard, who send Gen. Lucas Alexander to question her involvement in Lorn V conflict, thus following her to Kronus. Gorgutz has the skull of Crull, meaning they finally faced off just like the final Ork mission.