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Upon completion, the team felt that Alien Crossfire was somewhere between an expansion and a full-blown sequel.
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Other than the aliens, the Pirates proved to be the toughest faction to balance because their ocean start gave them huge advantages. The team also used artwork, sound effects, music, and diplomatic text to set the aliens apart. Chris Pine modified the AI to account for the additions. The developers eventually provided the aliens with 3 Battle Ogres the Mk1, the Mk2 and the Mk3, a Planetary survey, non-blind research, and other powers to produce "a nasty and potent race that would take the combined might of humanity to bring them down". They strove to make them feel significantly different to play, but still compatible with the existing game mechanics. The team believed the "coolness" of the Progenitor aliens would determine the success or failure of Alien Crossfire. The team had several goals: factions should not be "locked-in" to certain strategies players should have interesting things to do without unbalancing the game, and the factions must be fun to play. The first "call for features" was posted around April 1999 and produced the Fletchette Defense System, Algorithmic Enhancement, and The Nethack Terminus. The internet community provided "invaluable" feedback. He wanted to provide "builders" with the tools to construct an empire in the face of heated competition. Train wanted to improve the "build" aspects, feeling that the god-game genre had always been heavily slanted towards the "Conquer" end of the spectrum. The idea of humans inadvertently caught up in an off-world civil war focused the story. The backstory evolved quickly, and the main conflict centered on the return of the original alien inhabitants.
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The premise allowed them to mix and match old and new characters and delve into the mysteries of the monoliths and alien artifacts. The team considered several ideas, including a return to a post-apocalyptic earth and the conquest of another planet in the Alpha Centauri system, before deciding to keep the new title on Planet. The development team included Train as producer and designer, Chris Pine as programmer, Jerome Atherholt and Greg Foertsch as artists, and Doug Kaufman as co-designer and game balancer. Alien Crossfire features seven new factions (two that are non-human), new technologies, new facilities, new secret projects, new alien life forms, new unit special abilities, new victory conditions (including the new "Progenitor Victory") and several additional concepts and strategies. A month after Alpha Centauri's February 1999 release, the Firaxis team began work on the expansion pack, Sid Meier's Alien Crossfire.
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