The Cast stare at Hetepheres, aghast at the revelation of the Artist as her father. Finally, the Artist abruptly turns to James and says, "This is your fault for not rescuing me from that Nazi TARDIS faster."
The statement appears to devastate the young princess, at which the Artist apologizes, explaining he never knew she existed and he had to adjust to all of this. As the discussion continues, Emilie guesses that the Queen is the Artist's wife, an assertion he does not deny. When pressed for an explanation, he delivers the following theory as the princess leads the group out of the city:
His wife Zeidu, a strong psychic, managed to transfer her consciousness when the Daleks executed her. Unfortunately, the only body available at the time was another Dalek. She remained trapped inside a Dalek body for Rassilon knows how long, connected into their shared consciousness and forced to exterminate her own kind, going slowly insane, until an opportunity for escape came in another Time Lord woman, Persephone, who Zeidu was forced to execute. Rather than killing Persephone outright, Zeidu pulled her shot and stole Persephone's body. Now completely insane, confused, and obsessed, she took the name The Queen of Time, and escaped the war in its final hours. The Artist theorizes that it was during his captivity in World War II China that the Queen impregnated herself using genetic material she'd taken from the Artist.
The Cast think that their only option is to kill the Queen before she wakes up Sutekh; the Artist and Hetepheres will have none of it. Hetepheres, for her part, doesn't believe that her mother is capable of the horrific acts of which the Cast accuse her. She simply wanted to meet and help her father, to see if he really was the coward who abandoned her and her mother that she was always told he was.
Hetepheres knows very little of what the Queen is up to, though she says bashfully that her boyfriend had suspicions of experiments on his people. It then is revealed that Hetepheres is having an affair with Khama, the young Canaanite who helped the Cast and is now a Time Lord. The Artist attempts to prepare his daughter for the fact that Khama is changed.
The Cast make it back to the TARDIS and have a brief scare when James goes to collect Khama and the boy is no longer in the Zero Room. They manage to trace the boy's bio signature to the Cloister Room, where he's looking around in wonder, having simply gone exploring after leaving the zero room and not finding anyone around. Hetepheres has to be convinced that the boy is her beau, and that she, too, will one day change her face the way that he has. The Artist launches into a treatise on Gallifreyan biomechanics and physiology, and Chuck follows along for awhile, while Hetepheres actually seems to understand it all. Susan and the Artist note that the girl seems to have been educated in advanced biology, technology, physics, and Gallifreyan history through "myths" and "Bedtime stories" her mother has told her throughout the girl's life. Despite all of this, Hetepheres is floored at the idea that her mother has a place like the Artist's TARDIS somewhere.
Don and Emilie head outside to toke up, after which Emilie goes to her room and dyes her hair bright purple.
Khama informs the Cast that there is something going on underneath the pyramid, that the priests have been taking people from the slave community at the behest of Asherah, their goddess, beneath the sands. Most never return. He also insists that the priests are not human, that they're some kind of monster. When showed a photo of the Drosmians, he identifies them as the true appearance of the priests. He agrees to lead the Cast to the Sphinx, where the priests enter, but doesn't know how they'll get past.
The Cast, however, know. The Artist and Emilie use megaphones combined with her singing and his sonic screwdriver, while Susan sends telepathic screams at the four Drosmian guards, incapacitating them while Don and Davan dispatch the creatures. James grabs a khopesh on the way in. The Artist and Susan manage to access the entrance with the use of their sonic screwdrivers, and Chuck uses his to help them seal the door behind them.
When they reach a central chamber with four passageways leading off, Emilie focuses her psychic senses and discovers down one tunnel what appears to be a medical lab, with subjects strapped to tables, some dead, some deformed and dying, some quite alive. Down another she sees a plain chamber with a sarcophagus, an anachronism that doesn't belong down here at this time. Down a third she sees a strange, blue and green tunnel filled with a green mist. Down the fourth, she sees a figure she instinctively knows is the god Seth, and feels him tugging at the edges of her consciousness, calling her forth. She manages to break the psychic connection. The Cast, save a very stoned Don, decide they definitely are not going to see the god, who the Artist identifies as Sutekh. Don really wants to go, because, "Man, seeing a god! That'd be totally cool, man!"
The Artist shoots Don up with a stimulant to sober him up, after which he realizes that going to see the god probably isn't such a good idea after all.
The Cast heads for the med lab, where the Artist finds a log book detailing all of the Queen's experiments and plans for creating a new Gallifrey out of the human race and Earth. They examine a dead Dalek kept preserved in formaldehyde. As they begin to work on freeing the imprisoned slaves, the Queen's voice rings out, congratulating Hetepheres for bringing the Cast to her.
Hetepheres insists that her intent was not to lead the Cast into a trap, that it wasn't true. The Cast turn on her, until Emilie steps forward, insisting she has a feeling that Hetepheres is innocent and hasn't betrayed them.
The Queen tries to mentally dominate Emilie, Don, Davan, James, and Chuck, and all resist her efforts. Finally, in a rage, she steps into view, in the doorway, and says, "At least I can rid myself of your whore." She points a wand of some sort at Susan and fires an energy beam at the woman. James jumps to knock Susan out of the way, but is too late...Susan disintegrates before the Cast's eyes.
Davan and Chuck react instinctively. Davan hurls his khopesh at the Queen, sticking her in the ribs, as Chuck leaps on top of the woman, bearing her to the ground in a choke hold. The Artist, overcome at seeing his friends apparently trying to kill his wife, kicks Chuck to knock him off. James steps forward and knocks the Queen unconscious. Davan cleans and sutures her wounds while the Cast bind her and the Artist places a psychic inhibitor on top of her head.
Don and James step out to explore the strange tunnel while the Cast waits for the Queen to awaken. Don ties a rope around his waist, and James waits at the end of the tunnel, in case Don needs pulled back. James is shocked when, after a few moments, the rope is jerked through his hands at a strength he's never known, and he loses it all. Panicked, he turns and runs back to the Artist to inform him that he's lost Don.
In the tunnel, Don feels a sense of extreme vertigo and stumbles forward a few steps, then notes that the rope has gone slack. Continuing forward, he falls into what appears to be a high-tech observatory situated in the middle of some kind of red desert. Out the windows he can see a black night sky, and two silver pyramids. He contacts the Cast with his cell to let them know he's okay (thank you, Universal Roaming) and begins to transmit pictures. He's shocked when the Artist informs him that he is now somehow on Mars! The Artist also informs him that, based on what he sees from the pictures Don has taken of the controls and computer screens, that the Drosmian mother ship is in orbit around Earth, and in communication with the observatory (which is not Drosmian in origin, but Osirian).
The doors to the observatory swish open and two Drosmians enter. Don leaps back into the tunnel before they see him and returns to Egypt.
Back in the lab, the Queen awakens and the Cast interrogate her to no effect. She catches them off guard when, having slipped her bonds, she hurls the chair at Davan, catching him square in the face, and dashes out of the room, appearing to walk right through a wall, after a buildup of psychic energy, though she never removed the psychic inhibitor the Artist placed on her head. The Artist reasons she's clearly tapping into Sutekh's power, somehow.
Chuck and the Artist examine the wand with which the Queen shot Susan and dropped when she was taken down by Chuck and Davan, and determine that it is not in fact an offensive weapon but some sort of transmat, probably designed to send the victim to a random point in space-time. Anything more specific, the Artist needs the TARDIS facilities to work out.
Emilie again reaches out with her psychic senses and manages to intuit that the Queen is headed for the room with the sarcophagus, which the Cast has already reasoned must be her TARDIS. They give chase. When they enter, the Artist is shocked to discover that she's turned her entire ship into a Black Hole Converter, which could create a new Eye of Harmony directly under the Great Pyramid...or could just open up a black hole that swallows the entire solar system. He begins, with the help of Chuck's scientific knowledge and Emilie's postcognitive powers, to reverse-engineer what the Queen did, looking for a way to stop her. The three of them discover that this converter is tied into the Pyramids of Mars, and drawing energy from Sutekh and the pyramids. They work out a plan whereby they can, with someone stationed on Mars, connect with the observatory and create a bio-feedback wave that will not only destroy the black hole converter, but take out the Drosmian mother ship at the same time. Davan volunteers to man the console on Mars, since he's acquired some knowledge of alien systems operations and can, they reason, at least be talked through what has to be done. Don and James decide to go along to guard his back from the Drosmians at the observatory. The Artist then gives Don a megaphone and a spare sonic screwdriver, instructing him to use it through the megaphone and through the comlink to the Drosmian mothership.
The three men enter the observatory through the space bridge to discover there are now three Drosmians in the room. They quickly dispatch the creatures using the screwdriver/megaphone combination, and Don directs the sound blast through the com unit while Davan gets instructions from the Artist on how to set the controls to generate the wave they need.
The Artist, as he works, detects an opposing influence; the Queen is trying to re-route controls to an auxiliary control room. He traces her panel and directs Chuck and Emilie to go after her while he fights for control here. They rush off.
He fights with the Queen for a few moments but she wrests control from him. Finally, he determines if he can't keep control here, he'll count on Chuck and Emilie to distract the Queen from noticing...and sends all of his work to her control panel, then runs after the two.
On Mars, Davan uses the sonic screwdriver ("setting 46-A," the Artist tells him) to seal the doors so no more Drosmians can enter, and tells Don and James to get back to Earth to help out there. They head back and race to the Queen's TARDIS.
In the Auxiliary chamber, Chuck and Emilie catch the Queen off guard; Chuck grabs her in a choke hold while Emilie sprays her with mace. Unfortunately, Chuck doesn't avert his eyes quickly enough and ends up blinded as well. The queen sends a burst of power out in a wave around her that throws Emilie and Chuck in opposite directions; Emilie notes that the Queen's ring glowed for a split second before the blast and yells to Chuck to get the ring. The Queen levels a blast of energy at Emilie, drawing upon Sutekh's power to do so, and then calls in reinforcements: three jackal-headed servants of Sutekh enter. Two attack Emilie and one attacks Chuck, who is just getting his vision cleared.
The Artist enters the room and, seeing the servants of Sutekh, shoots all three with the space-time transmat, then heads straight for the control panel. The Queen screams, "NO! You will NOT destroy my work!" and pulls out a sonic blaster, which she shoots her husband with. The Artist, a smoking hole in his ribcage, staggers to the console, and says, "Yes, I will. I'm sorry," and hits a button on the console, then rasps to Davan through the cell phone link: "NOW."
He then drops to the floor, unmoving and un-breathing, just as James and Don make it to the control room.
Chuck throws the body guard aside and tackles the Queen, wrestling with her for the control ring she wears. James rushes over and tears the ring from her hand.
On Mars, Davan activates the controls, and a white beam of energy connects from the two pyramids and fires off into space, towards Earth.
Back on Earth, the entire TARDIS begins to violently pitch and shake. Rock, metal, plaster, and machinery begin to fall and cracks spider web up the walls. Don grabs the Artist's body and makes for the exit, Hetepheres in tow.
The Queen continues to fight, and finally, in desperation, Chuck picks up the sonic blaster and fires. The Queen falls to the floor, a smoking wound in her chest. Chuck, James, and Emilie dive out of the way as the ceiling comes down, burying the Queen's body beneath it. The three of them make their way out of the self-destructing machine.
The Cast notice the Queen's TARDIS enveloped in a blinding, crackling beam of energy as they stagger away from it, the beam piercing through the bedrock and into the open sky above, where the remnants of the Drosmian mothership can now be seen with the naked eye, burning up on entry. They work their way back to the Sphinx entrance, where they see Khama waiting with the assembled (freed) slaves while Davan aims a sonic screwdriver at the door, having reasoned that if 46-A is "lock," then 46-B must be "unlock."
It works, and the Cast stagger out into the desert, to see the disintegrating bodies of drosmian soldiers enveloped in streams of white energy coming from the same source as that immolating the Queen's TARDIS and their mothership.
Emilie uses her psychic powers to try and jump-start the Artist's hearts; he gasps at the Cast to get the hell away from him...and regenerates:
They help him back to the TARDIS while Khama leads the slaves away.
Back at the TARDIS, the Artist recuperates from his regeneration in the Zero Room, then considers leaving Davan and Chuck on Earth after their attempt to kill his wife. However, with convincing from his daughter and the Cast, and unaware that Chuck shot the Queen in the end, decides that they simply reacted to the situation in the lab on instinct and shouldn't be blamed. When he asks what happened to his wife, the Cast simply tell him she was buried when the TARDIS came down.
James asks about the new Time Lords running around, and the Cast reason that with the scarcity of information about ancient Egypt, the ubiquitous belief in magic in this era, and the harsh lifestyle and violence of the period, that people with the uncontrolled power of regeneration will end up being written into myths and don't endanger the timeline all that much.
As for Hetepheres, the Artist invites her to come with him and she agrees, setting up one of her handmaidens to take her place in Egypt.
The Artist returns to 2007 Pittsburgh and offers the Cast a chance to take their leave if they wish. Of the group, Davan decides to remain behind, his mission for Aegis complete (the Artist is not a threat to Earth) but tells the Artist, "If you ever need me, you know where to find me." Chuck wishes to continue adventuring with the Artist, but asks for time with his wife. The Artist agrees to return for them in a few weeks' time (by their reckoning) and pick them up. He bids them farewell, and departs with his daughter for places unknown...