Meanwhile (as much as you can have a meanwhile when you're in a vessel that flies beyond the normal reaches of time and space), the Doctor is playing K-9 at chess when Leela comes in. She challenges the Doctor to demonstrate his control of the TARDIS, and to actually navigate them somewhere on purpose. And, from the TARDIS memory banks, she chooses Exxilon. The Doctor, cautious of what happened last time, gently navigates the TARDIS around the first beacon, only to run right into the newly activated one, landing the now-powerless TARDIS right on top of the Great City. First, the Exxilons shoot at them with bows and arrows. Then, after a bit of negotiation with the group, and as Bellal can almost recognises the Doctor, the marines are upon them, with guns. Gizlan holds Leela hostage with a poisoned stick, even as she and the Doctor try to convince him that they aren't with the marines, and their deaths mean nothing. Indeed, her life is only saved when Mark, using his android aiming skills, shoots the spear from his hand. He then promptly glitches out, falling unconscious after a debrief with the disgruntled Captain Barnard.
The Doctor and Leela are taken prisoner onboard the Earth flagship as they blow up the new beacon, and potentially the TARDIS with it. Luckily, Anya, having traveled with the Doctor (in her past, but his future) has smuggled it aboard, and through a series of voice disguises, her second-in-command Ellasi Craig, and a data-pack to interface with K-9, she's able to convince the Doctor to examine Mark Seven, after he sabotages the engines, stranding them in deep space. Using a mental interface, the Doctor is able to discover that, on his last mission deep undercover in Dalek HQ (posing as a Roboman), Mark was discovered, and his programming modified to include the Dalek Protocols. They couldn't fundamentally change his directive to protect life, so they altered it to include Dalek life at the forefront, and programmed him to believe that the Daleks were also dying from the plague, and needed half the parrinium mined to survive. The Doctor (after almost falling for the Dalek Protocols thanks to the mind link) is unsure of this - the Daleks could easily want to destroy the parrinium simply for the blow it would strike against their enemies.
Mark awakens, having been jolted by the Daleks monitoring his condition, who are now aware the Doctor is on the scene. They try to have Mark kill him, but K-9 is able to chase him off, just as the Daleks arrive on scene, with Mark to greet them. Anya and the Captain debate courses of action, and while he's surprised at Mark's betrayal, Anya isn't. The whole reason she was here was to keep an eye on him after he returned from Dalek HQ acting strangely. They go to face them as they board the ship. The Daleks begin to shoot everyone, but Captain Barnard is able to trap them behind a bulkhead. Even as Leela, Anya and Mark are on the other side. The Doctor phones up the Dalek Supreme, bluffing that the Captain will blow up the ship before he lets the Daleks have the parrinium, and asking whether they really need it. The Supreme rebuffs him, and prepares to deploy a weapon that will destroy all the unshielded organic life aboard the human ships. Then, they can take the parrinium and go home.
Anya and Leela try to convince Mark that the Daleks are playing him, but his programming is falling apart, and he heavily injures Anya. When the Daleks do bring out their death ray, he snaps and rewires it. Now, everyone will die. Human, or Dalek. With this threat hanging over them, the Supreme reluctantly admits to the Doctor that, yes, the space plague mutated into a form that affects the Daleks. The Doctor berates them for going to all these games to both take the parrinium and sabotage the humans, rather than just asking for help. The Supreme taunts them that at least they're running away to survive Mark Seven's rewired death ray, and they flee. Fortunately, using the mind probe from earlier, the Doctor is able to link to Mark Seven again and convince him to shut it down, saving them all. Mark Seven himself then shuts down to perform full system diagnostics.
In the sickbay, Leela visits Anya. She questions how Anya knew so much about the TARDIS, about K-9... how she knew her name. Anya admits the truth, that she travels with the Doctor after Leela is gone. and begs Leela not to tell the Doctor. Leela says that she does not keep secrets, but is obviously touched by the similarity they share. And indeed in the TARDIS, she pretends not to know Anya's name when the Doctor asks who she was.
The Dalek Protocol contains examples of:
- Canon Immigrant: Mark Seven, as previously featured in Terry Nation's Dalek Annuals, and Big Finish's adaptation of his planned Dalek spin-off, The Destroyers, plays a main part. Of course, due to release order, he first showed up alongside Anya in The Diary of River Song Series 8, but this audio occurs first.
- Have We Met Yet?: So for Anya, the events of The Fourth Doctor Adventures have already occurred. Meanwhile, Four is traveling with Leela, which takes place before he meets Anya.
- Improbable Aiming Skills: Mark shoots Gizlan's spear out of his hand, while the Dalek Supreme is ordering him to shoot the Doctor
- MacGuffin: The Parrinium, much like Death to the Daleks. It cures the space plague, but since there's no victims here, it's simply what motivates the Daleks and humans to fight.
- The Slow Path: Bellal is much, much older than we'd seen him previously, while the Doctor looks as young as ever. Of course, a regeneration helps keep a Time Lord looking young.
