The film begins with Selene narrating the events of Underworld, Underworld: Evolution and Underworld: Awakening that have set the stage for the events of Underworld: Blood Wars.
At the point in time at which the film begins Selene is still on the run, trying to evade both the Lycans and the Vampires that have betrayed her. The Lycans are after Selene in the hopes of using her to discover the location of her daughter, Eve, whose blood could hold the key to creating an army of Hybrids. However, the Vampires are seeking to bring Selene to justice for her role in the deaths of the Vampire Elders Viktor and Marcus Corvinus. Selene’s only allies are her progeny David and his father Thomas.
A Death Dealer is seen riding through the streets of Prague on a motorcycle and they try to escape from several Lycans; the Death Dealer ultimately fails to evade their pursuers. In an abandoned warehouse a group of Lycans are attempting to subdue Selene in order to capture her. Fortunately David appears just in time to help Selene to defeat her would be captors. However, during the fight one of the Lycans, Gregor, is able to shoot David in the stomach and the wound doesn’t begin to heal.
David informs Selene that the Lycans have a new leader by the name of Marius; Marius is far stronger than his predecessors and is hunting Eve for her blood. Gregor, though wounded, is still alive. Selene tells him to pass a message along to Marius: he will never find Eve and not even Selene knows where she is. The Lycan attempts to answer back but Selene shoots both of his feet. The pair manage to find a safe house to examine David’s bullet wound and find that it still isn’t healing. Upon further examination Selene finds that the bullet is self-propelling and is still moving through David’s body faster than he can heal the damage. When she removes the bullet, Selene is surprised to find that it is emitting UV radiation. She proceeds to stitch the wound while telling him how she and Eve parted ways; they also take the opportunity to replenish their supplies.
At the same time as Selene and David are dealing with David’s wound, the main Lycan force is taking shelter in an abandoned industrial plant; Marius proceeds to tell them his plans and then chastises Gregor for failing to apprehend Selene.
Meanwhile, Thomas arrives at the castle stronghold of the Eastern Coven where he is greeted by a young Death Dealer by the name of Varga. He is then granted an audience with the leader of the Eastern Coven, Semira and tries to convince her to pardon Selene for her crimes, insisting that she was left no choice but to kill Viktor and Marcus. As a another incentive, he also reminds Semira that Selene is an experienced warrior and could prove herself to be a great asset, suggesting that she could train the Eastern Coven’s comparatively young and inexperienced Death Dealers. Semira calls a meeting of the coven’s Elite Council – Cassius, Hajna, Istvan, an unnamed woman, and Semira herself; Thomas is also in attendance to present his case. Eventually the coven agrees to offer Selene amnesty in exchange for her training the Death Dealers. The offer is presented to Selene via a letter from Thomas to David.
Selene and David arrive at the Eastern Coven’s castle in an armoured car with blacked out windows. Thomas and a number of armed guards accompany them into the castle where they are greeted by Semira. Semira then arranges a grand reception in Selene and David’s honour. Following the reception Thomas and David converse near a relief carved mural that depicts a battle between Vampires and Lycans; elsewhere it is revealed that Semira and Varga are lovers.
Selene accepts the Eastern Coven’s offer of amnesty. She begins to train the coven’s Death Dealers but Varga intrudes on the training session, commenting that no matter how hard one trains it is nothing like a real battle. He offers to spar with Selene as a demonstration; she will the play the role of a Death Dealer and he will play a Lycan foe. Within minutes of the sparring match beginning, Varga subtly cuts the palm of Selene’s hand with a previously concealed knife, the blade of which has been coated in nightshade. Within seconds, Selene becomes paralyzed and falls to the floor, and as she loses consciousness she sees Semira approaching her; Semira tells her that she will not forgive Selene for Viktor’s death. As soon as Selene is unconscious, Semira orders Varga to shoot the other Death Dealers who are present, an order that he quickly complies with. It is around this time that Semira’s motivations become clear: she was once Viktor’s favourite, his regent even but she was sent away after Selene was turned and still harbours a deep seated anger towards her.
Selene is taken to Semira’s quarters where she is placed into a machine that is designed to execute her by draining her blood; Semira intends to drink the drained blood and take Selene’s strength and power for herself. Fortunately, before too much of Selene’s blood is drained, Thomas and David come to her rescue, having worked out what Semira was planning. Semira engages Thomas in a sword fight as David tries to free Selene from the blood-letting machine. Varga soon appears and joins the sword fight against Thomas, distracting the older Vampire long enough for Semira to strike a fatal blow from behind. David, having freed Selene, escapes with his mentor by jumping out of the window, revealing to Semira and Varga that her is immune to the effects of sunlight. The escaping pair steal a car and escape from the Eastern Coven.
David gives Selene some of his blood in order to aid her recovery and they decide to seek refuge with the Nordic Coven, as per Thomas’ previous instructions. Meanwhile, Semira has already deduced the pair’s eventual destination as only the Eastern Coven and the Nordic Coven still remain and has dispatched troops of her own to the other coven; the troops are lead by one of the remaining Death Dealers, Alexia. However, Alexia has turned traitor to her own kind and become the lover of the Lycan leader Marius. Alexia discovers the stolen car the David and Selene have since abandoned and determines the route that they are taking to the Nordic Coven; she then meets with Marius. While Alexia and Marius are tracking Selene and David back at the Eastern Coven’s castle, the blood the Semira drained from Selene has been cleansed of any remaining traces of nightshade and is now safe for consumption. Varga adds a small amount of the blood to a goblet of water; Semira drinks the concoction and begins to transform.
Selene and David arrive at Vador, the stronghold of the Nordic Coven. Upon entering the fortress they meet Lena, the Nordic Coven’s greatest warrior. Lena takes the new arrivals to meet her father, Vidar, the leader of the coven. Vidar tells David that the mother he never knew is none other than the now deceased Vampire Elder, Amelia. Vidar then gives him a silver sword that belonged to his father Thomas; even so David refuses to believe it. When David leaves, needing time to think things through, Vidar gives Selene a vial of his mother’s blood to give to him; the blood contains Blood Memories of the capture of the first Werewolf, William Corvinus and Amelia fighting alongside fellow Elders, Viktor and Marcus, proving to David that Vidar is telling the truth.
Suddenly the Nordic Coven finds themselves under attack by a Lycan army, led by Marius. David and Lena help the rest of the coven fend off the Lycans. Outside the fortress Selene engages in single combat with Marius on an iced over lake. During the fight he asks Selene where Eve is, promising that he will not hurt her, that he only needs some of her blood; Selene refuses to give him an answer. Marius changes form and it becomes clear that Marius is no ordinary Lycan; Marius is a Lycan-Corvinus Strain Hybrid. Selene manages to land a blow with her sword but Marius shrugs it off and causes her to drop her weapon. Marius continues to attack, resorting to using his fists and physically throwing Selene about. By this point, Alexia has joined the fight, aiding her lover. Once Selene is weak, enough Marius retakes human form and continues to interrogate her concerning Eve’s whereabouts; Selene insists that she has no idea where her daughter is. Alexia picks up Selene’s sword and tastes the small amount of the other Vampire’s blood that remains on the blade; the blood memories that she witnesses indicate that Selene is telling the truth. In a fit of anger Marius shoots Selene and she falls through the ice. The Lycan forces retreat from Vador. Upon Alexia’s return to the Eastern Coven’s castle she is brought before Semira to present her report, confessing that she is Marius’ lover; Semira informs Alexia that she has always known of Alexia’s treachery and was using her for her own purposes before killing the younger Vampire.
David chooses to leave the Nordic Coven and return to the Eastern Coven, believing that it should be led, if not by one of the original Elders, then by someone of one of their bloodlines. Upon his arrival David informs the Elite Council of his parentage, presenting himself as the rightful heir to the Eastern Coven. Semira has no intention of losing her power and status to David and demands that he be arrested, only to find herself being arrested by none other than her own lover, Varga. She is subsequently imprisoned in the Castle’s dungeons. While Semira is imprisoned the coven comes under attack by Marius’ Lycan army. Initially the Vampires are able to effectively resist the Lycans, however, soon enough the Lycans use grenades to blow holes in the castle’s walls, letting in sunlight. Many of the Vampire die as the sunlight begins to hit their forces. David continues to fight, only to find himself face to face with Marius.
All of a sudden, Selene appears on the battlefield, the ends of her hair now white and wearing the type of coat worn by the Nordic Coven over her normal Death Dealer uniform. The Nordic Coven revived her and in doing so enabled her to develop new abilities. She swiftly begins dispatching the Lycans left, right and center. As she does so the rest of the Nordic Coven, led by Lena, also appear on the battlefield, ready to aide their brethren. While Selene is making her way through the castle, the guards in the dungeons are killed and Semira is inadvertently released from her cell. Selene and David find Marius in the dojo and Selene starts shooting at him. However, David is waylaid by Semira who attacks him with a short halberd in one hand and a sword in the other.
As Marius and Selene’s fight continues, a drop of Marius’ blood lands on Selene’s lips. She suddenly sees a series of blood memories in which Marius finds Selene’s missing lover Michael during the latter’s escape from the Antigen Headquarters. She sees Marius capturing Michael and slitting his throat in order to collect his blood and consume it. It is clear to Selene that her lover and the father of her child is almost certainly dead. She bites her own wrist; using her own blood memories of the time she has spent with Michael, Eve and David to fuel her rage. Although Marius has transformed, Selene rips out his spine, killing him instantly.
While Selene has been fighting Marius, David has still been struggling to fend off Semira, already having been wounded by her. He is able to damage a wall enough to allow a single shaft of sunlight to enter the room and land on Semira. While she is marvelling at her own immunity to the UV radiation, David stabs her through the head from behind, just as she had killed David’s father, Thomas. When David reaches the dojo he decapitates Marius’ corpse and shows the severed head to the remaining Lycan forces. Upon seeing that their leader is dead, they retreat from the castle.
In the aftermath Selene, David and Lena are chosen as the new Elders. Another narration from Selene begins as she comments on having gone from being an outcast to one of their chosen leaders and how they may have reached a time of peace and a chance for what is left of the Nordic Coven and Eastern Coven to heal and regain their strength. Then, briefly, it’s shown that during the time that Selene spent with the Nordic Coven after being resurrected, she was reunited with Eve.