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In order to save themselves, the trio must explore the huge alien ship and solve a large number of mind puzzles, such as connecting colored laser-beams with mirrors, unlock a door with rotating shapes, playing an advanced form of connect-the-dots with a computer interface, and one combat sequence, battling aliens called Krin. The puzzles are mixed with acting sequences from Carrere and Bocher, whose interaction with the player creates some light-hearted comedy. Numerous alternate scenes and clips were filmed and edited into game play. The alternate scenes appear depending on the player’s choice of game play.

During the exploration of the alien ship, Ari and Zack enter a Central Hub containing six doors in the shape of hexagons. They explore areas of the ship behind each door but do not find any navigational controls. However, Casey finds six purple orbs (one in each of the six areas behind the six doors). The orbs cause the beam of blue light and fountain of white lights in the middle of the Central Hub to fade away as a diver’s suit shaped device with a cannon on top of it appears. Ari and Zack insert the orbs into it, Casey brings part of an alien’s hand from the ship’s Sick bay (which is behind one of the Central Hub doors) and places it on the device. It activates an elevator which takes Ari, Zack and Casey up and out of the Central Hub.

The alien ship approaches the Sun and temperature inside starts to rapidly increase. Outside, the remaining Krin flee the ship, but some of them are destroyed in the heat. The elevator brings Ari, Zack and Casey into a control room where the device (which the orbs were inserted into) vanishes, revealing a fish-shaped shell. Ari and Zack notice a live alien and Casey goes over to communicate with it.

It is noteworthy that three endings were filmed:

The alien ship reaches the Sun and the Artemis burns and explodes in the heat.

The alien doesn't respond to Casey and Zack shoots it with his laser gun. The alien knocks Zack aside and attacks Ari. Ari kills the alien and the shell hatches into the Queen alien. Ari kills it and Casey changes the course of the ship, steering it away from the Sun. Ari assumes that Zack is dead and cries over his body, telling Casey that he was wrong about there being no such thing as a hopeless situation.

The alien responds to Casey and as the alien ship reaches the star, a force field appears around the Artemis and protects it from the intense heat. The fish-shaped shell turns out to be an egg, which hatches into a giant red alien Queen. The live alien, Ari, Zack and Casey bow to it.

In a voice over, Ari explains that the force field created by the creatures which called themselves "Seddy" protected them and the ship from the intense heat. The Krin either fled or were destroyed and the new Queen possessed "race memory" and being able to speak and know; she helped Casey’s translation abilities, answered many of Ari’s and Zack’s questions and repaired the Artemis. Zack receives a transmission from the Daedalus, wishing them a safe voyage and may their paths cross again. Zack tells Casey that he was right about there being "no such thing as a hopeless situation" and tries to convince Ari to join him on the mattress in the station room. Ari says nothing, and Zack murmurs, "Or not," as the Artemis speeds off into outer space.