Later on in the campaign, a party of Fremen diplomats are sent to Caladan, where they and the Duke Achillus are under attack by Tleilaxu soldiers. Many of the starting missions revolve around forming an alliance with the Fremen. House Atreides' campaign involves regaining the trust of the Fremen, with whom they have had an uneasy relationship due to unspecified past events. While each campaign has the story ultimately culminating up to the battle with the Emperor Worm, the three campaigns have subplots revolving around each faction's intents to conquer Arrakis.

The victorious house then regains control of Arrakis and the spice melange and proclaims their side's leader Emperor of Dune. Eventually the player destroys the Emperor Worm, and the Guild's plan is foiled. It then becomes clear that a last-ditch attempt must be made back on Arrakis to destroy the Emperor Worm before he awakes, by using the Smugglers Guild to get back to Arrakis. They also release a mind influencing drug in all the remaining forces water supply on Arrakis to make them slaves under the Guild. After the last battle with any one of the opponent Houses on their home planet, the Spacing Guild (Guild of Navigators) leaves the victorious House stranded on the enemies' conquered homeworld, attempting to control Arrakis with House Tleilaxu by genetically engineering an Emperor Worm with immense psychic powers empowered by Lady Elara. Whichever House wins the war will become the new leader of the Landsraad, and its leader the new Padishah Emperor, Emperor of the Known Universe.Р”В®ventually, it becomes clear during the campaign that the Tleilaxu are scouring Arrakis with hidden motives, with various probes spotted collecting flesh samples from dead sandworms. The Spacing Guild has presented the three remaining Houses (the same as those in the previous games: House Atreides, House Harkonnen and House Ordos) with a unique challenge: a war of assassins on the planet Arrakis. Emperor Corrino has been killed by his concubine, Lady Elara, and the Landsraad has been thrown into chaos. Like Dune 2000 and many of the other Westwood games that came before it, Emperor features cut scenes filmed with live actors.Р”В®mperor is set shortly after Dune 2000. In particular, it is a sequel to Dune 2000, carrying on from where it left off, with several of the characters and actors returning. While Dune II was a totally distinct story to that of Dune, and Dune 2000 was a remake of Dune II, Emperor is a direct sequel to the previous games. It is the third real-time strategy game set in the Dune universe, following its predecessors, Dune II and Dune 2000. It is based in Frank Herbert's science fiction Dune universe. Emperor: Battle for Dune is a Dune video game, released by Westwood Studios on June 12, 2001.

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