In ‘The Day Of The Doctor’ we learn that UNIT screen all of the Doctor’s known associates. The stated reason being that they can’t allow information about the Doctor or the TARDIS falling into the wrong hands.
We learn that Clara herself has already undergone this screening process at the Tower of London.
Clara has no memory of this, which has two possible explanations. Either this hasn’t happened yet from her perspective (so there could be a future episode where she travels to a point prior to this story and undergoes the screening process) or, since Kate shows no surprise that Clara doesn’t remember this, the event was wiped from her memory.
The board has various companions on it, including Amy, Rory, Martha, Sarah Jane, Wilf, Rose, Mel and Nyssa. The implication is that all of them were underwent the same security screening but this doesn’t necessarily mean that they were brought to the Tower of London and had their memories wiped.
Certainly several of those on the board were already members of UNIT (Martha Jones and Sarah Jane Smith) or Torchwood (Captain Jack) so would already be under a certain level of confidentiality.
Clara however is a civilian and so it is likely that others, such as the Ponds, received the same treatment. Presumably this was done to avoid them telling the Doctor, who might object to what UNIT is doing to his companions.
The degree of scrutiny may vary depending on how much time the subject spends with the Doctor. For example Wilf only has a passing acquaintance with the Doctor, compared to others and so his security check might be less vigorous.
The fact they also have a photo of Kamelion suggest that maybe the robot wasn’t destroyed in ‘Planet of Fire’ and found its way back to Earth. Alternatively there could have been a period where the 5th Doctor was on Earth with Kamelion long enough for them to take him aside for screening.
Nyssa is a special case as she is an alien and so her detention by UNIT is even more suspect. One can only imagine how she felt being interviewed (interrogated?) by an organisation designed to combat aliens.
With the exception of the Clara most of the photos are understandably taken from production photos from previous episodes. It does raise the question of where UNIT is obtaining these images and at what point they are bringing in the companions for security clearance.
Could they have access to information recorded by the TARDIS scanners, just as the Time Lords were able to do in ‘Trial of A Time Lord’? It could be that Martha Jones was able to plant a surveillance device for UNIT at the end of ‘The Poison Sky’ or during ‘The Doctor’s Daughter’.
It is easy to understand how UNIT were able to screen those companions who live in the same time frame as the organisation. Clara and Ponds resided within the UK between their adventures with the Doctor, giving them plenty of opportunity to pick them up.
It is harder to work out when they might have spoken to companions who were constantly travelling with the Doctor and who ultimately ended up on other worlds or times (so interviewing Mel or Peri would be a problem).
There is of course the possibility that they were interviewed during adventures in the late 2oth and early 21st century. Even if we didn’t see this adventure onscreen it doesn’t mean there aren’t unseen adventures for this to occur in (as the audios and books show). It would seem odd since an adventure usually indicates that some crisis is occurring so would they really pull someone aside when they are needed?
Since they are also dealing with a time traveller there is no guarantee that they are bringing in the ‘right’ version of a companion. What if in their intelligence gathering process UNIT had discovered the 1980s photos of Clara in a Russian sub from ‘Cold War’ and picked her up before she met the Doctor in ‘The Bells of Saint John’? This would have been confusing for all parties involved.
What would the security process be for a companion? There main concern seems to be that they won’t pass the information on and that they won’t abuse their knowledge. This indicates they are looking at their moral character, their allegiances and who they associate with (who will likely be undergoing security checks of their own).
Clara is given top clearance so that indicates a standard for the other companions to met. It also means that they can be given information that UNIT doesn’t even trust the Doctor with (such as the black archive), even if they late wipe that knowledge.
What happens when a companion fails the security check? The easiest answer is that their memories of travelling with the Doctor are wiped completely, to prevent that information getting out.
This is problematic when you have companions that could resume travelling with the Doctor, which is the case with Clara. If they wipe their memories the Doctor will realise something is wrong immediately.
Would UNIT keep them under constant observation and intercept all their communications? Would they imprison a companion or tell the Doctor that he is no longer allowed to travel with them? No option is ideal.
This whole process does provide us with further insight into what UNIT feels is important. They don’t want the Doctor and the TARDIS to be common knowledge. Newspapers and publishers could find themselves preventing from printing anything about him, websites could be shutdown and even those who only met him briefly (such as Craig from ‘The Lodger’) would be advised not discuss what they’ve seen.
Within your own games this can come up in a number of ways. You can run through these security clearance screenings with any companion of the Doctor’s (or any other Time Lord PC that UNIT has an interest in).
Even if you don’t run the event itself it is likely that it has already taken place, the companion just doesn’t know it. They could learn about this later, particularly if they find a way to detect if their memories have been erased.
The consequence of this can be explored in your game. If the Doctor or Time Lord PC finds out that UNIT are doing this to his friends what will he do? Would he stop it or understand that it is necessary? ‘Inforarium’ showed that the Doctor isn’t above altering peoples memories to protect his secrets but we also know the Doctor can be a hypocrite.
Those running a UNIT campaign now have a new activity for the players. They can be tasked with bringing in companions to undergo security clearance, by force if necessary. This can be a good way to feature a whole host of former companions (and maybe some future ones) with plenty of opportunities for adventure along the way (maybe the UNIT soldiers arrive at the worst possible moment).
If the companions are asked about their adventures with the Doctor this can serve as a spark for new adventures. They might relate information about something that is going to happen in the near future or point UNIT in the direction of danger that still needs to be resolved (the Doctor doesn’t always tie up loose ends).
Time travelling PCs could stumble across an archive of these security clearances and investigate some of this information on their own. They might even find their own files, that not only do they not remember but contain information from their own future.