Synopsis
At the conclusion of Brood War, Kerrigan and her Zerg forces became the dominant faction in the Koprulu Sector, having annihilated the United Earth Directorate's Expeditionary Force, defeated the Terran Dominion, and invaded the Protoss homeworld of Aiur. However, after the conclusion of Brood War, Kerrigan retreats to Char, despite having more than enough power to crush all remaining resistance in the Koprulu Sector. In the four years leading up to the events of StarCraft II, she has not been seen or heard from by any of the other characters, although her ultimate attack may come at any moment.
Arcturus Mengsk has been left to rebuild the Dominion, and is consolidating his power while fending off harassment from rival Terran groups. Valerian Mengsk, a character introduced in the novel Firstborn, will play an important role in Dominion politics, due to his position as heir apparent to the throne. Meanwhile, Jim Raynor, whose role in the events of StarCraft and Brood War has been marginalized by the media under the Dominion's control, has been reduced to mercenary status, and has been shown to be doing business with the "Moebius Foundation", a new faction which is interested in ancient Xel'Naga artifacts. Chris Metzen, Vice President of Creative Development at Blizzard, has emphasized that by the events of StarCraft II, Raynor has become jaded and embittered by the way he was used and betrayed by Arcturus Mengsk. Other new characters to the series include Tychus Findlay, first introduced in the StarCraft II teaser cinematic, a marine who will be a member of Raynor's crew, and Matt Horner, Raynor's second in command, a character originally featured in the novel Queen of Blades.
Following the fall of Aiur and the death of their matriarch Raszagal, the Protoss have retreated to the dark templar homeworld of Shakuras. There, Artanis, a former student of Tassadar, is trying to unify the Khalai Protoss and the dark templar, who have nearly separated into a tribal mindset as a result of centuries of distrust. Zeratul, tormented over the murder of his matriarch, has disappeared to search for clues to the meaning of Samir Duran's cryptic statements regarding the Protoss/Zerg hybrids in Brood War's secret mission "Dark Origin".
Plot
It has been four years after the conclusion of the Brood War, and the Dominion is once again the dominant Terran power in space. For reasons unknown, Kerrigan gathered the whole of the swarm at Char, and has vanished from sight. With the Zerg gone, the Protoss have once again taken a passive role in the galaxy. After the Brood War, Jim Raynor has formed a revolutionary group named Raynor's Raiders in order to overthrow Dominion Emperor Arcturus Mengsk. However, Emperor Mengsk has launched a massive smear campaign against Raynor, painting him as a terrorist.
The game begins in Mar Sara, where Jim Raynor is drinking away while waiting for his troops to get ready. Provoked by a televised press conference held by Mengsk, Raynor leads his forces to liberate the people of Mar Sara. After the battle, Raynor is approached by his old friend Tychus Findley, who claimed to have escaped from prison serving a sentence for a crime Raynor was also guilty of. Tychus proposes that Raynor's Raiders collect Xel'Naga artifacts for the Moebius Foundation, a scientific organization who will pay Raynor the funds he needs to wage his war against the Dominion. Raynor agrees and steals an artifact piece from the Dominion at a dig site in Mar Sara. As they prepare to leave Mar Sara, Backwater Station suddenly becomes under siege by Zerg forces. After escaping, Raynor then discovers that the Zerg have become active again with a full invasion of all Terran systems. However, the Dominion forces have largely withdrawn to defend its core worlds, leaving the fringe colonies to fend for themselves.
Afterwards, Raynor may choose to take side missions that focus around the plots of individual side characters:
After rescuing Dr. Ariel Hanson and a number of refugees from Agria, Raynor helps Hanson relocate the refugees while protecting them from the Zerg. However, when the Protoss arrive and reveal some of the refugees are infested, Raynor must decide whether to protect them until Hanson can devise a cure or purge the infestation. If he protects the refugees, the Protoss leaves and Hanson stays behind with the refugees. If he purges the infestation, Hanson herself becomes infested, forcing Raynor to kill her.
With Gabriel Tosh, Raynor obtains a number of resources to help Tosh reform the Spectres, a group of enhanced but mentally unstable Ghosts. The final objective is to break Tosh's fellow Spectres out of a high security prison on New Folsom. However, Nova arrives and tries to convince Raynor not to trust Tosh, as he is too dangerous and unpredictable. If Raynor decides to help Tosh, he gains access to Spectres and Tosh joins the Hyperion crew. If Raynor helps Nova, she gives him data on how to train Ghosts and later assassinates Tosh.
Matt Horner organizes a number of missions designed to strike at the Dominion. After recovering a recorded transmission proving Mengsk was responsible for the Zerg attack on Tarsonis, Raynor strikes the UNN headquarters on Korhal and transmits the message across the entire Dominion, causing a major scandal.
Raynor and Tychus raid a number of worlds to recover Xel'Naga artifacts for the Moebius Foundation. Eventually, the Zerg begin attacking the Moebius Foundation's main headquarters, prompting Raynor to assist them. Horner meanwhile doesn't trust Tychus and begins investigating, confiding to Raynor that Tychus' suit is rigged to shut down his internal organs when a certain signal is sent, confirming that Tychus is hiding something from them.
During this time, Zeratul sneaks onboard The Hyperion and gives Raynor a crystal with his memories in it. Raynor sees Zeratul searching for a prophecy about the half-Protoss, half-Zerg species found in the bonus mission in Brood War. However, Kerrigan is also looking for the prophecy and Zeratul barely manages to escape alive. Being unable to translate the prophecy, he takes it to another world to be interpreted. However, he finds that the Protoss he was looking for had been enslaved by a hybrid. He learns that the prophecy spoke of a "great hungerer", the overmind, and returns to Auir to try and read the Overmind's memories. While preparing to enter the Overmind's corpse, Zeratul encounters Tassadar, who tells him that the Overmind planned its death, and that Kerrigan was the key to saving the universe. Tassadar then shares with Zeratul the Overmind's prophetic vision of the future, which shows a great battle between the Protoss and the Zerg. The Terrans have already been exterminated, and the Zerg have been enslaved by the hybrids. The Protoss put up a valiant defence, but eventually fall to the never-ceasing numbers of the swarm. Zeratul then tells Raynor that he must protect Kerrigan, lest the whole universe be destroyed by the "Fallen One", who was actually the controlling force behind the Overmind's actions to dominate the Protoss.
After collecting the final artifact piece, Raynor's forces encounter Dominion battleships at the rendezvous point with the Moebius Foundation. Mengsk's son, Valerian Mengsk, reveals himself to be the owner of Moebius and tells Raynor that the artifact could possibly turn Kerrigan human again. He asks Raynor to help him invade Char and use the artifact to save Kerrigan and weaken the swarm. To the dismay of the crew, Raynor agrees. The crew is initially upset about working with the Dominion, but Raynor eventually convinces them that the mission is for the good of humanity. As the invasion of Char begins, The Dominion and Raider fleet is caught off-guard by a preemptive strike by the Zerg. Raynor then solidifies a position on Char and rescues any stray Dominion soldiers who crash land around the planet. The combined forces push towards the main Hive Cluster of the planet, and are attacked by endless waves of Zerg and Kerrigan herself. Eventually the artifact reaches full power and goes off, destroying all Zerg within its radius. Raynor's team finds Kerrigan, who has indeed turned back into a human.
Tychus, however, aims at Kerrigan, and reveals that he made a deal with Mengsk; he would trade Kerrigan's life for his freedom. Raynor protects Kerrigan from Tychus' rifle and kills Tychus with his revolver. Raynor is then shown walking across the battlefield with Kerrigan in his arms.