Utopia is basically a set-up episode. Russell T Davies has got his season finale all worked out, and needs to get all the pieces in place. The main thing is to resolve the series story arc, which this year has been the frequent mentions of one "Harold Saxon". He's the Master, so we have to introduce him. Rather than have him appear fully formed, we are instead introduced to a seemingly kindly old man. He's called Professor Yana.
The Master story arc has actually been going on for a lot longer than "Harold Saxon", which first featured on a newspaper in 2006's Love & Monsters. It begins with the Year 5 Billion trilogy and the Face of Boe.
It's merely a bizarre background character in The End of the World (a rip-off of the Navigators from Dune) but in the next series - in New Earth - the Face starts hinting at a secret it needs to share with the Doctor. By Gridlock the Face is dying, and so finally imparts the secret - "You are not alone".
For watching fans, this was obviously a reference to another Time Lord still in existence. The Doctor had always maintained that he was the last, and that he would know if any other of his kind still lived. However, this series had just shown us the Doctor conceal his biological identity using a Chameleon Arch - which hid his true self in a fob watch.
All the clues were there as to who the big bad would be for the Series 3 finale, and how they would go about explaining it. The villain would be another Time Lord who had been hiding behind another Chameleon Arch. Series 1 had reintroduced the Daleks. Series 2 had brought back the Cybermen. So Series 3 could only be leading us towards the return of the Master - his alternative identity, Yana, derived from the initials of "You Are Not Alone".
RTD also needs his monsters for the finale, and these derive from the end of the Universe. This, therefore, provides the setting for Utopia. We have to have the last remnants of the human race, right at the end of time, still seeking somewhere to survive - the fabled Utopia. This all sets them up to become the Toclafane, who will come back through time to almost destroy their own predecessors. That would be a paradox - how can they exist if they destroy their ancestors? - so a mechanism to create and maintain a paradox is required. As well as providing a nice cliff-hanger, with the Doctor, Martha and Jack trapped on a remote planet without a means of escape, the episode has the Master steal the Doctor's TARDIS. He's lost his own, so needs a way to get to the 21st Century, and it will also provide the means of creating the paradox needed to facilitate the Toclafane plan.
Chantho's role is simply to give the Master a companion, in the same way that the Doctor has a companion. He'll get another in the finale - a wife this time - and Chantho's "killing" of Yana is there to foreshadow Mrs Saxon's "killing" of his next incarnation.
Captain Jack was first introduced into the series to be a soldier, as there was going to be a battle with the Daleks in the first series finale - a role unsuited to the Doctor or to Rose. He is reintroduced here for similar reasons, having been off enjoying his first series of Torchwood. Martha will be leaving Doctor Who in a couple of weeks, but she is going to get a trio of Torchwood episodes to move on to - so Jack's appearance here helps introduce the two characters to each other and so get that out of the way now.
Utopia opens with the TARDIS landing in Cardiff Bay - taking us right back to Series 1 and The Unquiet Dead and Boom Town, with the Rift being introduced and later able to refuel the ship. Martha recalls an earthquake in the city (which was in the latter of the two Series 1 Cardiff-set stories). The final episode of Torchwood's first series had seen Jack hear the TARDIS materialisation sound whilst in the Hub. The implication there, however, is that the TARDIS lands within the Hub (the place is left in a mess as a wind blows through it), whereas here we see that the ship has arrived in the plaza above, and Jack has had enough time to put his overcoat on and grab the Doctor's severed hand (from The Christmas Invasion).
Whilst most of the episode is drawing together various story strands, and setting up others, Utopia still has to function as 45 minutes of adventure in its own right - which is where the Futurekind come in. They are the episode's villains, designed to make things interesting while all the structural stuff is going on.
The episode title derives from Utopia - a 1516 book by Sir Thomas Moore. It tells of a fictitious island and describes its socio-political systems, as well as its economy and religion. It strives to present the ideal form in each of these areas, which is why "utopia" now means a perfect situation.
In the Doctor Who episode, the people going there believe the sky is made of diamonds - as people were once said to believe that the streets of London were paved with gold.
The young character Creet who talks about the diamonds is played by the winner of that year's Blue Peter / Doctor Who competition. For Series 2, the prize had been to create a monster for the series, but for Series 3 RTD thought they should up the ante and have a prize of an appearance in the series for one lucky young winner. The runners-up also feature as non-speaking children in the same scenes. The winner was John Bell of Paisley, who has gone on to feature in the second and third Hobbit movies and the Outlander TV series (both of which have Doctor Who connections).
It was only later that RTD claims he was told that 'Mister Saxon' was an anagram of 'Master No Six'. The Master started using anagrams when he was in his Anthony Ainley incarnation - either within the context of the story, or behind the scenes, attempting to conceal his presence in a story.
If John Simm is Master No.6, then Roger Delgado is No.1, Peter Pratt and Geoffrey Beevers have to combine to be No.2, Ainley is No.3, Eric Roberts is No.4, and Derek Jacobi is No.5.
As Yana opens the fob watch we hear snatches of dialogue by previous Masters. The clearest is Delgado, from The Daemons.
The Doctor is impressed with the last of humanity about to launch into space, and describes them as "indomitable". This is a reference to The Ark in Space, which also featured the supposed last survivors of the human race.
Saxon was simply a name which RTD liked, and he had tried to launch a soap in the 1990's called "Saxon House".
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