At the time of writing this, the Doctor undertaking missions for his people is strictly a Classic Series Thing. It could be entirely possible that we will see this phenomenon taking place at some point in the New Series - but it hasn't happened, yet. It doesn't help that, during most of the New Who Era, the Time Lords were believed to be extinct. It's hard to receive missions from a civilization that you think has been destroyed! But now that they seem to have returned to our Universe - the Time Lords may start dispatching him again. In fact, it's entirely possible that whatever is in that mysterious Vault might have something to do with a favor that Gallifrey needs him to do. We'll find out soon enough, of course. But, at this point, when we speak of Time Lord Missions - it will relate to stories strictly from the Classic Series.
PROTOCOLS AND MOTIVES
With the exception of a few flashback sequences, the whole of the Doctor Who series concerns adventures that have transpired since the Doctor left his home planet and became a renegade. For the first six seasons, he appears to be flying completely under the radar of his people. When they do finally catch up with him - the Doctor is given his freedom at a price. Even during his exile on Earth, he is allowed some travelling privileges if he's willing to accomplish certain tasks on their behalf. After his full mobility is restored in The Three Doctors, the High Council (or, perhaps, the CIA - it's difficult to ascertain) continue to give the Doctor missions. A bargain seems to have been struck after the First Omega Crisis where he is allowed to break one of the greatest laws of his people but only if they can use him from time to time for their own purposes. We see him accomplish a few missions for the Time Lords during his Fourth Incarnation and one more time during his Sixth.
From the viewpoint of the audience, these missions for the Time Lords appear to start for the Third Doctor and carry through to the Sixth. The Fifth Doctor never seems to have to do any jobs for them and the work seems to finally completely peter out during his seventh incarnation. But, if we look a bit deeper, we see that this special arrangement between the Doctor and his people extends much further than first realized.
Another important point that I will try to raise is that these missions all seem to have a certain pattern to them. The Time Lords go about recruiting the Doctor in a certain manner and only engage him for very specific reasons. Essentially, his missions all have a certain set of protocols and motives within them. We'll break all of this down into very specific categories as the pretentious essay progresses. But first, let us define what a mission for the Time Lords actually is:
As usual, one of the best ways to define my point is to state what it isn't (if that makes any sense!). There are any number of occasions where the Doctor interacts with Time Lords and even goes about trying to accomplish something with them - but this does not constitute a specific mission given to him. In Deadly Assassin, for instance, the Doctor decides he must discover who the true killer of the former Lord President is. But it is a mission he chooses to undertake rather than one that is handed to him. That scene in Terror of the Autons where a Time Lord meets with him briefly on the radio tower to tell him that the Master is at work on Earth, very much, feels like he's being assigned a mission. But, technically, he's just receiving a warning. There's a difference.
To be more specific: a mission from the Time Lords is when the Doctor goes out on an adventure that his people want him to have. Certain things will be accomplished in that adventure that will advance an agenda of some sort for the inhabitants of Gallifrey. Oftentimes, (but not always) the Doctor is actually being told that he's on a mission. That he's doing some sort of handiwork for them.
As he points out in The Two Doctors, using a renegade to accomplish such tasks allows the Time Lords to maintain their stance of non-intervention. If the Doctor's true identity is ever discovered, his people will deny that they even sent him. Officially, he's there quite unofficially.
THE FIRST MISSION: ODD MAN OUT
Okay, now that we have the definition in place - let's get into some serious analysis. As I have already stated, these missions seem to follow a very specific set of patterns. The one exception to this pattern is the very first mission that he undertakes.
To all intents and purposes, the very first mission the Doctor is given seems to take place in Colony In Space. It is only in later stories that we learn there were other adventures where the Doctor was working on the Time Lords' behalf. We need to take a bit more of a retro-active stance to truly identify his first mission.
Strictly as the chronometer flies, the Doctor's first true mission for the Time Lords takes place way back in his first incarnation. At the behest of the Lord President, the First Doctor is brought forward in his own timeline to help his second and third incarnation deal with a Black Hole that is draining all power on Gallifrey. It's safe to say, then, that the next time the Doctor is sent on a mission for the Time Lords would be in his second incarnation. I would guess that it would happen sometime before the conclusion of Season 6. Again, the recruitment process is done in the same way. He's plucked from the proper place in his timestream and brought forward to assist his third incarnation.
When both incarnations are brought back to their proper location in time and space, it is most likely that they forget the whole incident. It may be that the Time Lords erased their memory or it may be because this just naturally happens when too many versions of the same person start meeting up (as is mentioned in Day of the Doctor). Whatever the case, the Doctor's first true mission for the Time Lords will only be remembered after it has happened to the Third Doctor.
It is interesting to note that the High Council explain to the Master during The Five Doctors that they could not find the Doctor in any of his incarnations. It seems likely that the whole trouble with the Death Zone was going to be another mission for the Doctor. That, because power on Gallifrey was being drained again, they might have been observing similar protocols to the ones they had used during the First Omega Crisis. They may have been considering using multiple incarnations of the Doctor to solve the problem, again. Otherwise, why would they look into locating all of the different versions of him? Silly postulation, of course. But still entirely possible.
For more silly postulation about memory issues during The Three Doctors, check out this entry:
AFTER THE THREE DOCTORS
So, if we keep things linear in a weird retro-active manner, the next mission the Doctor goes on that we are able to see is in The Two Doctors. Most fans see this adventure as taking place in what is commonly referred to as Season 6b. This is believed to be a series of adventures that were, hitherto, unseen by the audience until Season 20. The basic premise is that the Second Doctor was snatched away from his trial during The War Games just before he could regenerate. He was secretly granted his freedom to travel in his TARDIS - provided he would occasionally perform secret missions for his people. It's a theory fandom came up with so that certain continuity glitches that occur in The Two and Five Doctors will make sense. I know it's a bit weird to have to look at continuity in such a weird wibbly wobbly manner - but it's something that the show does from time-to-time. Just look at what happened during the 50th Anniversary when we were asked to accept a whole new incarnation that we never knew existed! Doctor Who just likes to re-write it's own history now and again.
For all the confusion it creates, The Two Doctors does follow the patterns that all other Time Lord missions move along. So, from this point onwards, anytime the Time Lords enlist the Doctor's aid - we will see a certain level of consistency to how things operate.
Just so we're clear, here are all the stories that fit into this pattern:
The Two Doctors
Colony In Space
Curse of Peladon
Genesis of the Daleks
Brain of Morbius
Attack of the Cybermen
The first pattern we'll point out is how the Doctor is actually recruited to perform these missions. Aside from the weird way in which he is plucked out of his timestream in The Three Doctors, the Time Lords always seem to respect Gallifreyan Mean Time. They approach the Doctor in the most current position of his timeline and enlist his aid. The actual recruitment, however, occurs in one of two distinct manners:
We see this approach in The Two Doctors, Genesis of the Daleks and, to a large extent, The Mutants. The Time Lords make it very clear to the Doctor that the next adventure he is about to have is on their behalf. The best example of this is in Genesis of the Daleks - where a Time Lord briefly appears to the Doctor to explain to him that they want him to interfere with the early development of his greatest foe. The Doctor is under no illusion that this is not some random landing that he's having - the Time Lords are revealing to him that they have guided him to this point and they specifically want him to accomplish something for them. It's made even more clear that the Doctor is on a mission in Genesis because he doesn't even get to take his TARDIS there. The transmat beam he was travelling along was intercepted and he's brought to Skaro. It could not be made any clearer that he's working for his people in this story.
In the other two stories I've listed, the recruitment process is still overt. The Doctor still knows he's doing a job for the Time Lords. But it's not quite as clearly implied. At the beginning of The Two Doctors, we assume he's just had a similar confrontation to the one we saw in Genesis of the Daleks - it just didn't happen onscreen. But from the dialogue he has with Jamie, we can see that he knows he's undertaking a mission. So we assume a Time Lord communicated directly with him in some sort of manner to tell him what he had to do.
In The Mutants, a pod appears to the Doctor from out of nowhere. The Doctor immediately recognizes its purpose and knows he's about to embark on another mission for the Time Lords. This is why I consider this another Overt dispatch. He's been made clearly aware of the purpose of his next journey. The fact that he knows what the pod represents indicates to me that he has dealt with them before. Perhaps he's been assigned these pods during an unseen adventure or two in Season 6b.
This is the most frequently-used method for assigning the Doctor his missions. Right in the first few minutes of Colony In Space, we see a group of Time Lords discussing the need to employ the Doctor to stop the Master on Uxarieus. But they suspect the Doctor is too bitter from his exile and is unlikely to cooperate if they approach him directly about it. They just choose to manipulate the situation so the Doctor believes he's arriving at his next destination by his own free will. In some cases, like Curse of Peladon or Attack of the Cybermen, the Doctor works out the truth as the adventure proceeds.
During Brain of Morbius, he immediately suspects his people are interfering with his travels. He does, later, admit to Maren that he's not entirely sure that it wasn't just a technical fault that landed him on Karn. But, from other clues that we see, this probably was a mission from the Time Lords.
Although it's never stated onscreen, we do guess that the Doctor works out that Colony In Space was a Time Lord mission. When he sees that his TARDIS no longer works once the Master has been thwarted, he probably puts Two and Two together. Which is probably what helps him make the educated guess that he leaps to at the end Curse of Peladon. He now recognizes the pattern of Covert Recruitment since he's seen it done to him once before. This may also be why his next few missions are Overt. The Time Lords realize he won't fall for their tricks, anymore.
The reasons why the Time Lords decide to use the Doctor to break The Laws of Non-Intervention also follow some pretty distinct patterns. Once more, The Three Doctors is the one exception to the rule. The Black Hole that Omega is using seems to be a threat that really only affects Gallifrey (Omega does start talking about destroying the Universe in later episodes but the Time Lords aren't, necessarily aware of this). Aside from this one story, the Time Lords always enlist the Doctor's help for one of three reasons:
Massive Threat To The Universe
In terms of the Doctor's personal timeline, this one was displayed for the first time in The Two Doctors. The Doctor is sent to Dastari to discuss the suspension of the Kartz and Reimer time experiments. The Time Lords are sure that this particular branch of time travel technology will punch a very dangerous hole in the Universe and, quite possibly, snuff it out of existence.
In terms of how we've been watching the show, the first time we see this motive being employed is in Genesis of the Daleks. The Time Lords foresee a time when the Daleks will succeed in controlling the entire Universe. So they send the Doctor to the Dawn of their Creation to alter this timeline.
Finally, the damage the Cybermen would do to the timelines by preventing the destruction of Mondas in Attack of the Cybermen would be catastrophic. He is covertly maneuvered into preventing the catastrophe
Cleaning Up Their Messes
This problem occurs a few times with the Time Lords. While the Doctor chose to leave Gallifrey for benevolent reasons, other defectors didn't have the noblest of intentions. Sometimes, these evil renegades develop a plan so nasty that the Doctor's course must be specifically diverted to deal with them.
Colony In Space is the first time we see this. The Master has stolen some secret information that the Time Lords were safeguarding about a Doomsday Weapon on the planet Uxareius. Should he actually get his hands on the weapon, it could prove devastating for all civilizations in the Universe. So they temporarily free the Doctor from his Exile to deal with it.
The other time we see this motive is in Brain of Morbius. Certain that the former Lord President has survived his execution on Karn, the Time Lords re-direct the Doctor's TARDIS to take him there and deal with it.
This one is, perhaps, the most mysterious of all the motives. Every now and again, the Time Lords seem to see certain political moves that need to be made to keep the Universe the way they want it to be. We have no idea, exactly, why these things must happen the way they do. We just know that it's important to the Time Lords that they occur.
For whatever reason, the Time Lords deemed it necessary for the planet Peladon to join the Intergalactic Federation (Curse of Peladon). Just as they needed the Solonians to truly break free of the exploitation of the Earth Empire (The Mutants). We can hypothesize all we want for why these changes needed to be instituted, but we'll never know for sure.
Of course, these are the stories where it was made clear to us that the Doctor was being dispatched by his people to handle certain problems. But we know that the Time Lords can be very covert in the way they manipulate his travels.
Ever noticed how it seems almost too coincidental that the Doctor shows up at certain places and certain times to right certain wrongs? Could it be that there have been other missions that he has been sent on where the Time Lords were manipulating him so deftly that even he couldn't tell?
They might just be the only race in the Universe who could outwit him to the point where they could use him without him knowing. And they understand better than most how moral of a creature he is. They don't need to tell him to interfere and influence things for the better. They just need to plop him down in the proper environment and he'll initiate the necessary changes without any prompting. Perhaps my definition can be broadened. Perhaps the Doctor has been on far more missions for his people than any of us can know.
Points to ponder...