Just why did Nyssa collapse at the end of "Four to Doomsday"? (Anyone saying "because Nyssa hadn't been made a companion yet when the serial was written" — shh.) The Fifth Doctor isn't sure, either, and it has him worried — so he takes he back to her home planet, Traken.
Traken being unavailable in the present (the Master accidentally destroyed it in "Logopolis"), the Doctor opts for Traken several thousand years before Nyssa's time; before even the Keepers. There the foremost healer of the day, Shayla, diagnoses Nyssa with acute exposure... to evil.
The Doctor barely manages to stifle a snicker at this diagnosis, but Shayla is being perfectly serious. She goes off to inform the High Council about the young woman dying of evil poisoning and the off-worlder responsible for it. The Doctor is really not laughing now. The High Council isn't either, and prepares to kick Nyssa and the Doctor off the planet again. The Doctor gets into a religious debate about the subjective nature of evil before remembering his good manners. Since everyone on Traken is guided, garded and healed by the Source, the Doctor assumes that it's a mystical nonsense artifact. It turns out to actually be a supercomputer, which shields the planet from any kind of interplanetary contact (barring some essential trade). Religion is not only unknown on Traken, but actively banned, and all the old temples have been converted into utility buildings. While Nyssa relaxes in a temple-turned-spa, the Doctor lets Shayla smuggle him off-planet and into the base of a very evil warlord named Kwundaar, who supposedly can help Nyssa fully recover.
Kwundaar instead makes the Doctor scream like a child just by looking at him, gives him a high dose of Mind Rape, steals his memories, and uses those to set his invasion plan into motion. The Doctor manages to escape (as he finds out later, with the help of one of Kwundaar's officers) and he and Nyssa leave Traken as quickly as possible, change into swimming gear, sneak into the Source via the spa and change the planetary shield level to maximum. Fortunately, this works. Unfortunately, it was exactly what Kwundaar wanted them to do, since the shield now allows him in but no energy out. He immediately invades the planet. The Doctor is knocked out cold, but manages to tell Nyssa the new security code he entered for the Source.
Kwundaar turns out to be the ancient God-king of Traken, who 2500 years ago gave the primitive Trakenites technology in the first place. They used that knowledge to create the Source, decided that religion was silly, and kicked Kwundaar out of their planet. Now that he's come back, the Traken council members feel like a right bunch of idiots and decide to convert to him again, hoping it'll stop him from massacring the whole planet. (It doesn't.) Kwundaar eventually reaches the Source and uses Nyssa's mind to enter the code... only to find out that the Doctor had told Nyssa a different code, which directly links the Source's data to a specific mind when activated. The Doctor immediately becomes the first Keeper of Traken and defeats Kwundaar, although the warlord promises that more of his kind will come back to kill the Doctor someday. Nyssa decides to take that risk, promises the Doctor that she'll continue to travel with him, and Shayla becomes the second Keeper of Traken.
- Allegory: The Doctor's described as a serpent.. And Traken is paradise.
- Ancient Artifact: The Source is already old now, and it's 3000 years in the past compared to Keeper of Traken. Kwundaar witnessed it's creation, over 2000 years ago.
- Barely-There Swimwear: Supposedly.
- Batman Gambit: In order to make his plan work, Kwundaar is counting on the Doctor to do what he always does, and move heaven and earth to save Nyssa's life. He's also counting on the Doctor's insatiable curiosity.
- The Doctor pulls one as well towards the end; he gives Nyssa a flawed access code that Kwundaar forces out of her, which ends up empowering the Doctor with the Source instead.
- Battle in the Center of the Mind: The Doctor confronts Kwundaar in the source.
- Beware the Nice Ones: Nyssa overpowers a soldier and forces her to show the stun setting otherwise she would shoot to kill.
- Crazy-Prepared: Kwundaar has spent over 2000 years worth preparing for the invasion of the source.
- Dawn of an Era
- Deal with the Devil: "What will you do to save a life?"
- Decapitated Army
- Distressed Dude: The Doctor, continuously."Believe me, I know what being knocked out feels like. I should write a paper on the subject."
- Easily Conquered World: 20 minutes flat.
- Go Mad from the Revelation
- A God Am I: Kwundaar is already this, and then he taps into the Source, he turns this up to eleven.
- Hot Springs Episode: Invoked. Nyssa spends much of the episode relaxing in a spa and dancing the Charleston (again). But when she and the Doctor sneak into the source and she has to wear a bathing suit, she's very unhappy about the amount of skin she suddenly has to show. (The fact that the Doctor brought his own regular clothes in a watertight backpack, but not hers, doesn't exactly help to improve her mood. He eventually decides to be a gentleman and lends her his coat.)
- Idiot Ball: The Doctor demonstrates a major case of carrying it by refusing to leave Traken when he should and tampering with the Source in order to sate his curiousity about what Kwundaar said.
- "Jump Off a Bridge" Rebuttal
- Kneel Before Kwundaar
- Machine Worship: Bordering on it.
- Mauve Shirt: The smuggler
- The Mole
- My Master, Right or Wrong
- Nice Job Breaking It, Hero!Nyssa: "You've handed him the most powerful force in the universe."Doctor: "Yes, I'm rather afraid that I have."
- Nightmare Face: Kwundaar keeps his face covered. Seeing it makes the Doctor scream.
- Not-So-Omniscient Council of Bickering: With a grand helping of Opinion Flip-Flop.
- Not That Kind of Doctor: The Doctor, again
- Obstructive Zealot
- Omnicidal Maniac: Kwundaar plans to have the entire universe destroyed.
- The Omniscient: Kwundaar, by virtue of having Psychic Powers.
- Origins Episode: For the Keepers of Traken
- Outgrown Such Silly Superstitions: Traken.
- Perfect Pacifist People
- Physical God: Kwanduur is considered this.
- The Plan: The Doctor's plan to regain control of the Source.
- Psychic Block Defense: The Doctor claims he has these. It doesn't matter against Kwundaar who's powerful enough to break them.
- Psychic Powers: Kwundaar.
- Religion of Evil: Kwundaar-ism.
- Sequel Episode: To "The Keeper of Traken", in that the creation of the Keepers is depicted.
- Sequel Hook: By means of retcon. Nyssa falls ill at the end of "Four to Doomsday", broadcast some 20 years prior to this story being written. The original reason was that she was suffering ill effects from her experiences in "Four to Doomsday". Lance Parkin uses that incident but changes the cause to build this tale of Nyssa's return to Traken.
- Space Pirate
- Superior Species: The Trakenites view themselves this.
- The Scream: The Doctor screams like a child when he sees Kwundaar's face.
- Total Eclipse of the Plot
- Utopia: How the Trakenites view their world. They pity the rest of the universe because they can't live in such a perfect world.
- We Are as Mayflies: Kwundaar will remain.
- Why Don't You Just Shoot Him?: Kwundaar orders the Doctor shot on sight, as soon as He Has Outlived His Usefulness.
- Writer on Board: Nyssa's anti-religious remarks and the Doctor's anti-death penalty remarks could be construed as this. Neither character expressed such beliefs on the original television series.