Sam calls Mental on Stein's phone and is answered by Mental's daughter, Judy. With Ugh-Zan IV dead, the Time-Lock is then activated, displaying an inter-dimensional portal to 3000 B.C., the timeline where the Sirians became extinct. The struggle to this destination ends with Sam killing Ugh-Zan IV, the father of Ugh-Zan III from The First Encounter. Sam then makes one last travel to the Temple of Hatshepsut, where the Time-Lock is located. Now determined to finish what the Sirians started, Sam vows to use the Time-Lock himself and kill Mental in the past before he can destroy humanity in the present. Traversing through more tombs, Sam gets back in touch with Hellfire and learns that Mental's forces have overrun headquarters shortly before she is killed. Sam is relieved of duty and in the process of being extracted from Luxor, but his helcopter is shot down once again and he is forced to flee towards the lost ruins of Nubia. This is slowly accomplished and Charlie Team is ready for insertion into the Time-Lock. Once outside the pyramid, Hellfire arrives to extract Sam to Karnak, the location of the generators. The data from Sirian chamber reveals that in order to power the Time-Lock, two dormant but incredibly powerful plasma generators need to be activated. Once inside, he not only discovers the hidden chamber, but recovers crucial information and a bracelet device from the remains of what might have been Earth's last Sirian. From the riddles uncovered from the hierogylphs, Sam detonates the Sphinx with explosives, revealing a tunnel underneath the Sphinx and descends into the pyramid. Sam clears himself to the pyramid and makes it to the Sphinx. The scientists at HQ decipher the hieroglyphics which indicates a hidden Sirian chamber below the Great Pyramid of Giza. He makes it into the museum, recovers the data from Stein's phone and transmits it to headquarters. Sam's insertion goes haywire after his helicopter is shot down and both teams are quickly wiped out, leaving Sam the only survivor. Sam tells his squad they are are protecting professor Stein, a scientist carrying hieroglyphics believed to contain instructions for powering up the Time-Lock. Their mission is to recon with Bravo Team after they lose contact with HQ. Sam 'Serious' Stone, Captain of the Earth Defense Force, is dispatched with a small squad of soldiers to Cairo in Egypt, which has been occupied by Mental's alien army for sometime.

But as the device lies dormant, they must first discover a means to turn it on. Through it, that person could reach a pivotal point in time and assassinate Mental in the past and change the future for humanity. In a last-ditch effort, the survivors turn to the Time-Lock, a recently excavated device that, allegedly, is capable of granting a single person the ability of time travel via an inter-dimensional portal. This leads to a three year-long war that has driven humanity almost to the point of extinction. During this time, Mental, an extraterrestrial overlord, is awakened from dormancy by the humans and sends out his hostile alien armies to attack Earth. In the middle of the 21st century, humanity had begun to uncover artifacts and ruins left behind in ancient times by the Sirians, a long forgotten alien race from the planet Sirius. Team Alpha in a Black Hawk, on their way to the museum.

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