Boston Low serves as the central protagonist of the game. After Attilla transforms into a start ship and transports Maggie Robbins, Ludger Brink and Low himself to an alien world, the trio immediately begin searching their surroundings for a means of returning home.
After a second encounter with one of the mysterious ghosts, Low decides to dig near the ground where it vanishes, but turns the shovel to Brink when insisted that such an action should be handled by the Archeologist. However, the ground gives way and Brink falls in, dying instantly. The death leaves Low feeling guilty, but Robbins manages to convince him that it's not his fault and that there was no way to tell such a thing would have happened.
After discovering and activating the first tram system, Low finds himself at the Museum spire, where he finds strange morphing displays that give him hints about how many of the mysterious alien technology, including the strange green stones he finds and later uses to revive Brink. Meanwhile, Robbins spends most of her time in the adjacent library, researching the strange computer like device in the hopes of maybe learning the alien language.
After resurrecting Brink, he and Low stumble upon more of the green life crystals, the newly revived Brink showing a strange obsession with collecting more of the stones. When Brink vanishes, Low searches the other spires in order to find him, eventually coming across him at a cliff side cavern on the Tomb Spire. Brink, now singlemindedly set on accquiring more life crystals, shuns Low's attemps at pairing up to search for clues. Eventually, Low makes his way to a strange pyramid like tomb under the Tomb Spire and revives the Inventor, the alien responsible for creating many of the worlds technology.
However, when Low attemps to tell Robbins of his findings, a spide-like creature kidnaps her and Low is forced to blackmail Brink in order to get his help. On the Map Spire, in a darkened nest, Brink and Low manage to save Robbins by diverting water from a waterfall onto the spider creature. With Robbins safe, Brink savagely retakes his life crystals, which Low had used to get him to come. With Robbins tagging along, Low revisits the alien and the two are able to learn much of the world's history, including how it's inhabitants discovered a new dimension, Spacetime Six.
Low and Robbins learn that in order to return home, they will have to activate the Eye, the device that allows access to Spacetime Six. However, the control system for activation requires life crystals, which Brink has selfishly used every last one of on himself. However, it turns out that Brink is rebuilding the device that creates the crystals, and after an arguement with Low, agrees to split things "fifty-fifty". The device though, only manages to create two new crystals and when Low attemps to take them, citing that it's less than fifty-fifty, Brink snaps completely and tries to kill both Robbins and Low. But the ledge collaspes and Brink falls into the sea.
Before the alien device is activated, Low is forced by Robbins to swear that he will not use a life crystal on her in the event of her possibly dying. Ironically enough, Robbins is killed when device is activated, but Low presses on, determined to retrieve the other aliens from Spacetime Six, and have them build him a ship to return to earth. Entering the Spacetime Six, Low finds the aliens and manages to bring them back into our dimension, along with Brink and Robbins who are mysteriously revived.
The story ends with Brink, Robbins and Low returning to Earth on another starship, with the intent of telling the humans of Earth of the fantastic journey they shared.