Tony Lee used to write the IDW Doctor Who comic book, and was also credited with co-writing the Doctor Who/Star Trek crossover published by the same company. Before walking off the book.

But in 2013 he had been asked to pitch a sequel series, four months before IDW and the BBC would part ways and Titan would gain the license. And he gave them one with Doctor Who – and Star Trek: Deep Space 9.

It's only "fanfic" now. But it could have been…

STAR TREK: DEEP SPACE NINE / DOCTOR WHO – DOMINATION

An Eight-Part Story Pitch by Tony Lee

High Concept: When The Doctor and a time – augmented Sontaran Battle Fleet are thrown through a wormhole into the Alpha Quadrant, they find themselves facing the might of Deep Space Nine and the Federation. But when the Sontarans join with the Jem'Hadar, the Doctor must help Deep Space Nine stop this, taking the fight into the Gamma Quadrant and into the past where they meet the crew of the original Enterprise, while Clara finds herself in the midst of an invasion, forced to team with Quark to save the station while avoiding zealot Bajoran cults and Federation's Section 31…

Synopsis: The Doctor and Clara start the story having stopped yet another Sontaran plan for universal domination, but are being chased through the time vortex by the Tenth Sontaran Fleet. The Sontarans have tried to create Time Travel and failed, and the resulting connection to the TARDIS (by force field) has thrown them into a Wormhole, tumbling out of control.

Meanwhile at Deep Space Nine, currently in the middle of a long war with the Dominion (grey uniform season five) – Cardassia has just joined the Dominion, but the promenade is abuzz due to a recent archaeological find on Bajor – a temple dedicated to a mysterious blue box, based on cave paintings from millions of years earlier. The priestesses claim that this is the true Emissary – while Worf, seeing this recognises the TARDIS from the time he met the Doctor (Assimilation2) and prepares for the worst.

The wormhole opens and Deep Space Nine prepares for a Jem'Hadar invasion – but instead it is the TARDIS and a Sontaran Fleet that fly through! In the immediate battle with the defending station the Sontarans drop the force field on the TARDIS, allowing it to make a short term hop, crash landing onto the Deep Space Nine promenade. Deep Space Nine and the Defiant see off the Battle Fleet who escape back through the Wormhole and back into Gamma Space. On the promenade, the arrival of the TARDIS has created quite a stir, as some the Bajorans believe that the first Emissary has returned (thanks to the paintings) and, as the Doctor and Clara emerge, a riot breaks out. Luckily Odo and Worf manage to rescue the Doctor and Clara – Worf remembers the Doctor well. As he takes the two visitors to Captain Sisko, one of the Federation officers makes his way to a com station, sending a message to Earth and Starfleet Command – tell Section 31… the Doctor has returned.

In the Gamma Quadrant the Sontaran commander, Stye forms an alliance with the Jem'Hadar – two clone races uniting thanks to the mediation of the Vorta clone Weyoun, who realises that this new race will be a good diversion against the Federation. He is also interested in Stye's fixation in the TARDIS, time travel and the power it could give the Dominion.

With Worf vouching for him, the Doctor explains to Sisko the problems that the Sontarans could cause, in the process meeting Jadzia Dax who, due to her multiple Dax incarnations understands the Doctor better than anyone else – and claims that she met him once before, when she was Tobin Dax, but it's hazy. Sisko can see how this new race could give the Dominion a tactical advantage and agrees to send the Defiant (with the TARDIS on board) into the Gamma Quadrant to check for any information.

As the Doctor briefs Worf on everything he knows about the Sontarans, Clara wanders the station, finding her way into Quarks where she surprises the Ferengi with her cunning, winning a bet and his friendship. She also meets Doctor Bashir, who immediately falls for her. At this point a Cardassian warship appears, with Gul Dukat commanding. He demands to speak to Sisko on behalf of the Dominion – Sisko agrees. Dukat claims that the Dominion want the TARDIS, but Sisko refuses. The Doctor, hearing this is concerned – the only way the Cardassians would know of the TARDIS is if the Sontarans have told them, and if they want time travel, they might attempt again on the Sontaran vessel with catastrophic results. Dukat expected this though and agrees to tell his masters, but not before a shape shifter sneaks aboard the station.

The Cardassian ship leaves through the wormhole, but Sisko is suspicious and decides that the Defiant must leave immediately. The Doctor, worried now about the Sontarans new allies decides to come with them, bringing Clara and the TARDIS.

Clara meanwhile finds herself facing the shape shifter who stuns her, locking her away while assuming her form.

The Defiant, with Sisko, Worf, Jadzia and O'Brien leave DS9 for the Gamma Quadrant with the Doctor and 'Clara' with them. In the Gamma quadrant they find the Sontaran fleet, but the Defiant is cloaked and is able to get close. However a battle does kick off after the Doctor realises that 'Clara' is a shape shifter and, in the resulting confusion it manages to de-cloak the ship before it's destroyed. Surrounded by enemy vessels, the only way the Doctor can save the outnumbered Defiant is to link its shields to the TARDIS core and try to jump the entire ship out of phase – but as they do this the Sontaran ship begins to show signs of pre-Time Travel workings and instead, the Defiant and the Sontaran ship are pulled into the Time Vortex together.

On Deep Space Nine, they believe that the Defiant has been destroyed. Doctor Bashir discovers the unconscious Clara, learning about the Shape Shifter. As they make their way to the bridge however to inform Major Kira, they see that a Federation task force have secretly docked onto the station – Section 31 have arrived.

(NOTE: At this point, Section 31 are nothing but a myth, and these soldiers are not named by anyone else as the Section)

Section 31 manage to gain access to the Engine Room and through the computer system disable Deep Space Nine, locking Kira and the federation on the Bridge as they start to systematically hunt for the Doctor and the TARDIS.

The Defiant appears in the past, randomly thrown out of the vortex – the Sontaran ship isn't to be seen. As the crew start to make urgent repairs, the Defiant finds itself facing another ship – the USS Enterprise, NX-01, captained by Jonathan Archer! After the Enterprise confirm that the Defiant is truly an ally (harder to do after they see Worf on the ship) they explain that they're en route to a planet that's sent a distress signal, a cry for help from an enemy that sounds remarkably like the Sontarans. The two ships agree to team up, and while on the Enterprise the Doctor meets a visiting engineer, Tobin Dax, thus giving him an explanation of how Jadzia knew him as Tobin and Trip agree to lend a hand to fixing the Defiant.

On Deep Space Nine Bashir and Clara are found by Section 31 and are taken to the bridge which, now opened is placed under Federation law by Commander Connor, the man in charge of the invading soldiers. But, as the Section 31 agents argue with Kira, Odo realises that the way that the ship was able to gain entry onto Deep Space Nine without anyone knowing was because their agents disabled the sensors – and with no external sensors, Deep Space Nine are blind! As he realises this, there is an explosion – Deep Space Nine has been invaded by an attack force of Cardassians and Sontarans! Their mission – seize the TARDIS! Destroy Terok Nor!

Meanwhile in the past as the two ships travel through sub light space, Jadzia Dax meets Tobin Dax as O'Brien discovers that Hoshi Sato is the great great great great grandmother of his wife Keiko. Sisko and Archer talk about responsibility while the Doctor discovers Doctor Phlox.

On Deep Space Nine, with most of the Federation and Bajoran military held by Section 31, the Sontaran and Cardassian army are easily taking over. But, when Section 31 finally admit their mistake and start to fight back, Bashir and Clara are caught in the crossfire and make their way to Quarks, trying to work out how to get out of this. Odo shape changes into the TARDIS, purely to divert soldiers away, suddenly coming to life, a fighting TARDIS seemingly the Sontaran stuff of nightmares!

The Enterprise and the Defiant find the invading Sontaran vessel, only to discover that the Sontarans aren't in it, and instead a skeleton crew of Sontarans lead a troop of Jem'Hadar! On the planet, an away team led by Worf and Reed take them on in hand to hand and ranged fire battles!

Back on Deep Space Nine, as Bashir and Clara get to Quarks, a Cardassian attacks them but is knocked unconscious by Morn, and Clara has an idea to place Garak in Cardassian uniform – the Cardassians may know him, but the Sontarans don't and may take orders from him! Garak reluctantly agrees as the civilians of Deep Space Nine create a militia to help the Federation. Clara ends up making a rousing speech, gaining the Bajoran zealots to the cause as well, using any leverage she has with anyone to create this fighting force.

The crews of the Enterprise and the Defiant finally manage to stop the Jem'Hadar – The Doctor, Jadzia and O'Brien beam aboard the ship to disable the time-tech, and the Doctor discovers that this wasn't an accidental journey, the controls were set for this planet, this time! They disable the tech but the Sontaran crew refuse to be taken, detonating their warship as the Doctor, O'Brien and Jadzia escape by transporter. The Doctor feels that something worse is going on. He uses the Defiant data banks as he examines the planet, realising that the whole point of this 'invasion' was to decimate a part of the solar system during this time zone, a domino that leads to another. This planet was vital during the upcoming 'Enterprise timeline' Romulan war, and without it, Earth would have lost and the Federation would never have been created. Luckily, they were able to stop it, but it shows exactly why the Dominion can't ever have Time Travel! After a farewell to the Enterprise, the Defiant and the TARDIS return to their time.

However, Deep Space Nine is having a bad time of it. Klingons have arrived to assist them, and the Cardassians are fighting the Klingons. The remains of the Tenth Sontaran Fleet are being fought off by the small force of Bajoran and Federation ships, while the station itself is chaos. But Quark's militia, helped by Clara assists Odo in bringing much of the fighting to an end. But in one of the Cardassian warships Dukat wants to destroy the station and begins to set his weapons upon it – until the last minute arrival of the Defiant stops him!

With the Defiant and the Klingons together, the Sontaran and Cardassian ships have no chance and the Sontarans signal their surrender as the Cardassians escape. Having retrieved all the surviving Sontaran vessels, the Doctor wires their half created time circuits into a loop, throwing them into the time vortex until he has a chance to send them to their correct time. The Defiant goes to dock – but there's still a problem. For the Section 31 Commander Connor has taken Clara hostage, Federation rifle to her head and demands that the Doctor give him his TARDIS technology – or she dies.

Angry now, the Doctor enters the TARDIS, asking for a Federation survival pack to be brought to him. Sisko offers to stop this but the Doctor is adamant – he'll do this.

On the station the Commander counts down from three, about to execute Clara – as the TARDIS appears around him, bringing both Clara and Connor into the TARDIS console room. The Doctor explains that guns won't work in the TARDIS as he slams his controls, throwing the TARDIS into a time spin. By the time Connor gains his balance, the TARDIS has landed and Clara has clunked him across the head with the dropped rifle. The Doctor, furious explains that he can do anything to Connor, at any time. He can simply wink him out of existence, change his fate. He opens the door to ancient Bajor, a desert scape, throwing Connor out of the TARDIS with the survival pack – about a month's worth of supplies. He shuts the door, presses a switch, turns it off, opens the door again – and it's a month later, and a bearded, terrified Connor is welcomed back in, having spent four weeks alone on the planet. Connor's will is broken and he promises not to hunt the Doctor again. As the TARDIS leaves, we see the results of Connor's month in the past – a survival tent, scattered food and a wall drawing of the Doctor, Clara and the TARDIS, the same one we see millions of years later…

Back on Deep Space Nine, as Connor and his men leave with their tails between their legs the Doctor and Clara say their goodbyes and return into the Wormhole, which leads back to their own time vortex. With everything back to normal Jadzia smiles. It was nice to see the Doctor again. When Sisko mentions Tobin being on the Enterprise Jadzia nods, but points out that Tobin wasn't the ONLY Dax to meet the Doctor… he'll be back…

And on a planet hundreds of years earlier, a lone Jem'Hadar, the last survivor of his ship goes into hiding, his mission to destroy the future only just beginning…