Unlike the previous game, which was a platformer, this one is an Action-Adventure game, where the game is viewed over the characters shoulder. The player has to make their way through the levels.
Conrad Hart, after destroying the Hostile Alien Planet, he went into suspended animation in the Previous game. Half a century later, he is found and captured by the Morphs, and imprisoned in New Alcatraz. He is, however rescued by John O'Conner, who then gives Conrad a Handgun and other essential items. Conrad then sneaks around the base onto Johns ship. While escaping, Morph Ships attack them but the two quickly teleport to Shadow, a Mandragore Base, just as the ship is destroyed. In the base, Conrad is informed by members of the Mandragore resistance that while he was in cyrosleep, the Morphs made Earth Surrender. Conrad is sent to rescue Professor Bergstein from Asteriod D321. Bergstein gives them a Datacube, which contains a virus that can blow up the base, due to it containing a Mind Manipulating Weapon. This results in the whole asteroid being obliterated as well , however. Conrad travels to Pluto, where he meets Ageer, who explains his people want to join the Mandragore Resistance. He sends Conrad to Easter Island, where Ageer tells him that the Oracle will lead him to a Pyramid. The Super Morph, however ambushes him. He eventually however manages to enter the pyramid with the Oracle, and learns about Ageers Peoples History (They are an Ancient Alien Race). Returning to his ship, he sees John O'Conners speaking with the Master Brain, stating that his plan to infiltrate Project Shadow and plant a detonation device was a success. After noticing Conrad eavesdropping, John transforms into the Super Morph. Conrad fights through all the Morphs, and goes to the Control Room, and learns that the person with the disarment code for the detonation device is being held hostage by the Morphs. Conrad saves them, and recieves the codes before teleporting away. Conrad disables the Weapon, and they Mandragore rediscuss their plan. The Ancients give the Mandragore the knowledge of where the Master Brain is on Easter Island. After teleporting to he Master Brain, he throws the Oracle in front of it and leaves behind the Pyramid. The Ancients then acrifice themselves to destroy the Master Brain, and Conrad Flee's, but is chased by the Super Morph.
There are two endings, one where if Conrad reunites with Sarah, the Super Morph is killed, the ship flees from the island and joins a fleet of Mandragore ships. At Shadow, Conrad announces the tide is turning against the Morphs and that he is no longer alone.
If Conrad doesnt reunite with Sarah, he kills the Super Morph and escapes, with Sarah dieing on the Island. Although the Morphs are being beaten, Conrad's relations with the Mandragore are unknown.