- Zeratul. This is one of the primary Protoss characters from the original game who is over 100 years old. He has been exiled from Aiur because he did not submit to the Khala. In Brood War, he led a party of Protoss survivors to the homeworld of the Dark Templar Shakuras. Along with co-patriots, he devises a plan to revive the Xel'Naga temple to help rid the area of the infestation by Zergs. Although they do succeed in retrieving the crystals they need to revive this temple, Aldaris is killed. In the final episode of Brood War, Zeratul is blackmailed into slaying the new Overmind. He retrieves the matriarch who has been brainwashed, but is pursued by the forces of Kerrigan. In the final mission of Brood War, he starts searching for clues about a genetic engineering facility he discovers. This is likely to form part of the plot of Starcraft 2.

- Arcturis Mengsk. In Brood War, Mengsk becomes the leader of the Dominion. He narrowly escapes capture and becomes an ally of Kerrigan and Raynor. However, Kerrigan betrays them, crippling the defense. Mengsk builds special interest groups by calling in favors and attacks Kerrigan's base at Char. In spite of the help, Mengsk is defeated but in Starcraft 2, Mengsk and his son, Valerian, find the evil empire of the Dominion even though it is opposed by the foerces of Jim Paynor and other inferior groups.

- Artanis. Artanis is a Protoss advisor who works with Zeratul and Judicator Aldaris to help evacuate the surviving Kahlai to Shakruss and then stayed on to help them fight the Zergs who had infested the planet. They became furious with Kerrigan and helped to activate the Xel'Napa temple. In Starcraft 11, he will be the leader of the unified Protoss and will continue to struggle to reunite the people.

- Sarah Kerrigan. She played a major role in Starcraft and Brood War as a manipulator. At the end of Brood War, although her forces dominate her enemies and she is able to take over a dominant position in the sector. In Starcraft 2, she will be relocated to Char and even though she does have the power to wipe out her enemies, she choose not to. This creates an uneasy tension in the alliance.

- Jim Raynor. Although he only made a few appearances in Brood War, Raynor will play a significant role in Starcraft 2. He returns to wage war against Mengsk, but his forces are defeated. He has to resort to obtaining work as a mercenary and starts to drink heavily because he blames himself for losing Kerrigan to the Zerg. His hatred of Mengsk is also enhanced by a series of propaganda attacks that are fed to him by the Dominion. According to the creators of Starcraft 11, Ryanor will become a hero in this game.