Emperor is set shortly after Dune 2000. Emperor Corrino has been killed by his concubine, Lady Elara, and the Landsraad has been thrown into chaos.
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. 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.
Eventually, 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. 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. They also release a mind influencing drug in all the remaining forces water supply on Arrakis to make them slaves under the Guild. 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. Eventually the player destroys the Emperor Worm, and the Guild's plan is foiled. The victorious house then regains control of Arrakis and the spice melange and proclaims their side's leader Emperor of Dune.
Source: Wikipedia, "Emperor: Battle for Dune," available under the CC-BY-SA License.