Leaving the armory, Seo comes face-to-face with Gallifreyan guards, who arrest her and escort her through the capital. She manages to distract them, however, then slam the door to seal most of them away from her. She fights hand-to-hand and knocks out the rest, then races down to the lower vaults.
The Time Lords can't track her, as she doesn't appear on scans.
They try to lock down the capital, so that they can use the retina scan doors to either trap Seo or to figure out where she's going (if she manages to hack them). But instead, when they arrive where Seo's been "trapped", they find that Seo's forced the doors open.
When Seo is deep in the lower vaults, she stumbles across something that looks like a hypercube. Picks it up, and it's glowing and bright, like it's got something inside it. But it doesn't act like a hypercube, because there's no telepathic message.
At first, Seo is confused.
"What looks like a hypercube, but isn't one?" Seo asks herself.
Then she drops the cube, in sudden horror.
As she remembers what she knows of the events in "Paradox", and realizes that she knows exactly what that thing really is.
That's when the Time Lord guards finally find her.
Seo gets chased, but at the same time, she's thinking this through. When she'd picked up that cube, she could tell that it already contained a Time Lord soul. That was probably the only reason it hadn't sucked out her soul when she touched it — the cube was already full.
But if someone found the cube before her, and touched it — that means somewhere on Gallifrey, there's a Dalek in a Time Lord body.
There's a traitor on Gallifrey, and no one else knows about it.
The Chancellory guard chase her into a side room, and corner her. They insist she comes with them.
"There's nowhere left to run," they remind Seo.
Seo glances over, sees a door that nobody else seems to have noticed. She beams. "Except through the back door!"
Then she spins around, races towards it, and leaps through it.
The guards freak out.
Because that "door" wasn't a real door at all — it was a Matrix door, and one that can only be accessed by the President of Gallifrey.
But Seo just passed right through it!
...
"Call off the search!" Jenny cried. "She's not a criminal, she's my sister!"
"She somehow broke into one of the most secure vaults on Gallifrey," said the Castellan, "on a mission to — by your own admission — steal one of the most dangerous weapons we have on hand, and remove it from Gallifrey."
"But she did nothing," Jenny retorted.
"We only have your word for that," said Coordinator Landax.
Jenny turned on him. "What's that supposed to mean?"
"It strikes me that you two have been extremely well briefed for this mission," said the Coordinator. "You arrive here, from another universe, in a way not even we can discover. You two claim never to have been here before — yet you know our customs…"
"And your sister knew the codes to get into the inner vaults," the Castellan continued, "knew the Moment was stored, there, and now seems to be displaying an intimate knowledge of the lower foundations."
Jenny hesitated.
"I can't understand my sister," Jenny admitted. "But the reason I know so much is because I've done a lot of research on Gallifrey. I thought you were all dead, so I learned what I could out of respect, to keep your memory and traditions alive."
All stasers came out at once.
"Dalek infiltrator?" The Coordinator asked.
"Highly likely," said the Castellan, pulling the trigger.
A hand grabbed the Castellan's arm, making the shot go wide. A lean, tall man with dark hair stood in Gallifreyan robes, his eyes fixed on Jenny. No one had heard him arrive.
"I do believe that might be a little presumptuous," said the man, fishing a paper out of his robes and handing it to the Castellan. "Given the circumstances."
The Castellan stared at the note.
The Coordinator didn't lower his staser. "Cardinal Braxiatel, you have no right to stop—"
"I'm afraid he does," said the Castellan, showing the note to the Coordinator. "It's from the President."
The two looked the note over.
Then looked back up at Braxiatel.
"The President agreed that the facts were indisputable," Braxiatel said. He gestured at Jenny. "Her biodata confirms her identity. We have detected no trace of Dalek elements so far in her physiology. And — having been to the planet Messaline myself to acquire some rather exquisite sculptures — I can verify that her story, as much as we've heard of it, is true."
The Coordinator seethed.
"I am only repeating what the President told me," Braxiatel insisted, calmly. "Nothing more."
"And I suppose you had nothing to do with the decision yourself," the Castellan muttered.
Braxiatel held up his hands. "Heaven forefend!"
The Coordinator saw through it in an instant. Grabbed up the note and crinkled it into a ball. "I don't care if she is or isn't a Dalek agent," said the Coordinator. "She's an outsider, and that's just as dangerous!"
"The public sees the Doctor as a great hero," Braxiatel replied. "The President believes it would be unwise to—"
"The President — or you, Braxiatel?" The Coordinator snapped. Advancing on Braxiatel, glaring. "Oh, you may have caught the public eye with your lapdog Romana and her pet projects — but you don't know what you're asking us to risk. You didn't spend your lives fighting the Daleks!"
Braxiatel's face darkened. "I did fight in the War."
"Eventually," the Castellan muttered.
"And I had my reasons," Braxiatel said, sweeping over towards Jenny. "But as none of them concern this young lady over here, I believe we would be remiss towards our guest if I went into the details yet again."
The Castellan gave it up, and turned to leave — presumably to the President, to question Braxiatel's wisdom.
The Coordinator lingered a moment longer, to remind Braxiatel that, "I watched Arcadia fall — you didn't. I won't let that happen, again."
Then he left, too.
"Oh, but you are letting it happen, Coordinator," Braxiatel muttered, eyes still fixed on the door. "You already are."
Jenny was still a little disorientated by everything that had just happened.
"Who… who are…?" Jenny asked.
Braxiatel turned to her.
His eyes lighting up, all at once.
"So... you're the one," he said, examining her, curiously. "Yes, I can see the resemblance. Quite remarkable."
"Who are you?" Jenny said. "Why did you save my life?"
"Well, I could scarcely sit by and watch them shoot you down in cold blood," said Braxiatel, pulling up a chair to sit opposite Jenny. He stared at her a few moments longer. Studying her, like a connoisseur studying an artistic masterpiece. "Incredible. A Gallifreyan… born outside of Gallifrey. And, even more incredibly — a Lungbarrow. Like myself."
"A what?"
Braxiatel explains to Jenny that she is a member of his family. The Lungbarrow family.
Romana bursts into the room which holds Jenny and Braxiatel. Romana is absolutely furious. She demands a full biodata extract be taken of Jenny, immediately, and commands Braxiatel to stay very far away from her.
It's clear that Braxiatel and Romana had, previously, spoken about Jenny, and that Romana had gotten Braxiatel his audience with the President, leading to her pardon. However, Romana has also clearly seen something that's changed her mind.
Braxiatel tries to insist that this isn't necessary — "You can see she's a Lungbarrow. This is a family affair. That is all."
"Not anymore," Romana says.
She waves for a robot to enter, and it carries in the Ma'erissa, still glowing. Raises it up to show to all.
Everyone in the room starts backwards, immediately.
Recognizing it.
(The one we saw in Paradox was a prototype. This is a Type 4, and no longer requires a name on the outside. The real personality is eased into place over a foreign interior, so that while Daleks are stringing them around like puppets, the Time Lord appears to be normal.)
"The Chancellory Guard found this in the lower vaults," Romana says. "It's been activated. Someone on Gallifrey is has been taken over, and is working for the Daleks. And since it's very likely that someone is this person's sister… I think a DE scan is well overdue."
Jenny's biodata is extracted and compared to the Doctor's DE. It's pretty obvious, when this happens, that Jenny is telling the truth.
Moreover, the biodata extract tells that Jenny is a perfectly formed Gallifreyan.
Too perfect for any human-created progenation machine to have created, on its own.
(Romana figures out through the DE that Jenny hadn't been perfectly formed, when she first emerged. But that something had been planted inside the Source that would not just terraform the planet — but change the cells in Jenny's body so that she'd become a perfect Gallifreyan. This is why she wakes up, when the Source activates — the second the Doctor leaves, and time has a chance to realize Gallifrey's still around.)
This makes Romana suspicious — in a very different way. "An outsider," says Romana, "born outside of Gallifrey, but a perfect Gallifreyan. Born after the War — but the Doctor's daughter, so a natural hero to the people."
She turns to Braxiatel.
"If I didn't know you better, Braxiatel," Romana says, "I'd call this an astounding coincidence."
"I haven't the first idea what you mean," Braxiatel replies.
(Since Braxiatel has admitted that he's visited Messaline, Romana has worked out that Braxiatel himself probably helped create the Source, and altered it so that it would make Jenny a perfect Gallifreyan. He did this by communicating with one of his future selves, in typical Braxiatel fashion.)
Anyways.
Romana demands to know who Seo is and what's going on.
...
Seo slams the door behind her, and locks it. Then barricades it.
She looks around. Doesn't know where she is, but it looks like a long corridor. She keeps running, but gets the weird impression that something's wrong, here. Seo wonders if the Time Lords have chased her into a trap, and starts getting a little nervous.
Then resolves that she can't get nervous. If they've locked her into a trap, she'll just have to be more clever than them. Use their own trap against them.
She tries to get a better idea of where she is, and discovers all kinds of Time Lord secrets just lying around behind unlocked doors. Some of the doors lead to meadows and fields, others to Gallifrey's past, others to distant worlds, others to forbidden secrets.
Seo wonders why these Time Lords aren't locking up their secrets better! It seems very weird.
It all seems very weird.
Seo starts to wonder just where exactly she is. And how, exactly, she got there.
.
The President is summoned, but they all soon find that the Matrix has locked them all out. As if it's been barricaded against anyone else entering.
They find a way to track the data stream flowing out of the Matrix, but they can't enter it themselves or alter it in any way.
Their accessing the Matrix, however, winds up sending everyone into a panic. No one's sure how or why, but somehow, Seo's managed to get inside the Matrix, gain access to every scrap of data in there, unlock every door and every partition, and even change things at her own whim. This should be utterly impossible.
(Braxiatel must mention, somewhere, that it's peculiar that the Matrix seems to recognize Seo — as if she's been here before. Except that she hasn't.)
They demand to know, from Jenny, how Seo's doing this. Jenny isn't sure, but has a hunch based on what she learned about Gallifrey from her father and other sources.
"Tell me about the Key of Rassilon," Jenny asks.
The Time Lords explain it to her. The Key of Rassilon is the only way to gain full control of the Matrix, and since the Matrix is the computer system that controls everything on Gallifrey, it gives complete control of Gallifrey, as well.
"And it's a bit dimensional?" Jenny guesses.
"More than a bit," Romana replies.
"An incredible feat of multidimensional and trans-temporal engineering," Braxiatel confirms. "The Great Key is one of the most powerful items in the panopticon."
Jenny takes in a sharp breath.
Knows exactly what's going on, suddenly.
"Seo's also known as 'the Key'," Jenny explains. "She can act as, essentially, a master-key to fit in any dimensional lock. That means… she doesn't need the Key of Rassilon to take control of the Matrix. She can use herself!"
The Time Lords are all very alarmed at this.
They start to think that this is a trap or an invasion.
"No, wait!" Jenny says. "Look at what she's doing in there! Does it look like she has a plan? Or does it look like she's stumbled in and now has no idea where she is, or how to get out?"
It does look like Seo is lost in there.
The changes to the Matrix appear to be random.
The Time Lords decide they need to track Seo down and get her out of there as soon as possible. They decide to construct a scoop, based on biodata prints from the Doctor, Jenny, and anything they have on record that's a match for Seo, so they can physically extract her from the Matrix.
They all race off to do so.
Jenny proposes a simpler solution.
She asks if there's any way to get a message to Seo, inside the Matrix.