Spore/Space Stage

After the civilization phase, the space phase begins. The player may terraform and colonize uninhabitable planets with special tools that are purchased with credits (water tool, volcano tool, etc.) The ultimate power in that area would be a technology which Wright dubbed the Genesis device, named after the device in Star Trek II: The Wrath of Khan, both of which have the same purpose: transform a dead world into a planet capable of sustaining life in a matter of minutes. During the 2007 TED conference, Wright showed off the planetary effects the UFO can have, such as pumping carbon dioxide into the atmosphere to increase the amount of greenhouse gases, which over time caused the oceans initially to rise and flood coastal cities, then eventually evaporate and transform the world into an arid desert planet, followed by a molten rock in space. Wright semi-jokingly called it "a sequel to An Inconvenient Truth. The player may cause icy comets to crash into a planet to create water, or force volcanoes to erupt to increase atmosphere. Players may also colonize hostile worlds or deep under the ocean once they gain the ability to create bubbled cities, similar in function to self-sustaining arcologies. Once the world around them becomes habitable, the city loses the bubble.

The player may travel between star systems and make contact with other civilizations on distant worlds, most of which are created by other players. The player finds other sapient species by running the mouse over other star systems and their individual planets to try to pick up radio static or noise that can indicate intelligent life. When the UFO visits that world, they may impress the beings with fireworks, attack them with weapons, or try to establish a language with the civilization via a Close Encounters of the Third Kind-styled musical mini-game. These civilizations may react violently to the player or worship them, depending on that civilization's behavior and the race's personality. User-created races uploaded to the player's machine will behave as that user played them; that is, if a user played a race pacifistically, that user's race would behave in the same manner to the player. Conversely, if the user played that race as a malevolent species, it would be very difficult for the player to negotiate with that species. On a grander scale, the player could try to conquer the galaxy by different means, such as beginning an interstellar war, diplomatically creating an interstellar union and so forth. As a show of great force, the player may even use a weapon to completely destroy a planet (similar to the capabilities of the Death Star from the Star Wars saga), which will sometimes bring retribution from that species and its allies.

During exploration of other worlds, the player may scan content and add the information to a database designed like a trading card series called the Sporepedia. The player may also abduct creatures (familiar or unfamiliar, sapient or animal) and transport them to other planets. Players can do this to test a planet's inhabitants to see if they are friendly or not, or to merely test a planet's habitability. Conversely, the player may beam down his/her creature to interact directly with an alien species instead of through the UFO. The player may interbreed different species genetically, or place a monolith (in the style of 2001: A Space Odyssey) on a planet, triggering evolution of intelligent life, then come back later to see what has evolved. On lifeless worlds, the player may also find strange "artifacts" with unknown purposes to be used later on, possibly adding tools for the UFO.

In the E3 2006 demo, Will Wright explained that there would be over half a million different stars, each one having its own planets, more than anyone could visit in a lifetime. As is traditional with most of Will Wright's games, the game never presents the player with an absolute ending and the Space Phase continues for as long as the player wishes. The exploration remains fresh from uploaded content and on-the-fly procedural generation by the software. During the 2007 TED Conference seminar, Wright used accelerated time dilation during the Milky Way view to show the dynamics of the entire galaxy, as supernovae exploded in brilliant points of light, and the galactic arms slowly turned. He pointed out the nebulae, which the game features in real-life separate categories of planetary nebulae and reflection nebulae, each of which perform their actual functions in space. He also brought the UFO close to a black hole, keeping a cautionary distance from the structure.

The main unit of currency is, as with the civilization phase, Sporebucks, but there is also SPice for trading (There are multiple types eg. Blue, Yellow, Red etc.

"Sandbox" Mode

The Space Phase is sometimes referred to as a sandbox mode, because the player has near-complete control of everything. Rather than presenting the player with a finite goal, as earlier phases do, the Space Phase gives the freedom to accomplish any variety of tasks they wish to perform. It has been mentioned that the Space Phase works on two axes: a horizontal axis (the ability to interact with many planets in a variety of different ways) and a vertical axis (the ability to revisit different phases of gameplay).