- Char was described as being in a system with one visible sun, but both suns are visible in the between-levels artwork; the two suns are also discussed in StarCraft Maps of the Month.
- The sequence of events around the death of Zasz were very different. In the game, Tassadar and Zeratul had seemingly formed an alliance by this time, but were hiding from the Zerg. Kerrigan detected them with her newfound powers after leaving the Amerigo with the knowledge of the Ghost Program. Tassadar lured her into combat with an illusion while Zeratul slew Zasz.
- Zasz's Garm Brood was then destroyed by Zerg commanded by the player Cerebrate (this would be Kerrigan's personal Brood). In the novel, Zeratul slew Zasz before he even met Tassadar, the Garm were destroyed by Daggoth's Tiamat Brood, Kerrigan faced Tassadar many times before being fooled by the illusion (which happened after the death of Zasz) and used lines that occurred earlier in the game (when Zasz was being set up for assassination), and only later did Tassadar and Zeratul form an alliance.
- Later during the Zerg missions, Kerrigan destroyed a substantial portion of the Protoss base and slew many Dark Templar while holding aggressive conversations with Zeratul. Zeratul was later captured and had to be rescued from a terran installation. In the novel, Eye for an Eye is ignored and skipped with Zerg fighting Protoss much later and loosing the battle heavily rather than winning. The Protoss were then immediately "reinforced" by Aldaris and Artanis.
- Zeratul is repeatedly referred to as Praetor, rather than his correct rank, Prelate (though it is possible that the Prelate is the Dark Templar analogue of Praetor).