Judging by the first two series, it’s time for another Illicit Alien Technology episode, but you didn’t come here to read “see six weeks ago”, so let’s look at a different aspect of the semi-official alien hunting gig. Semi- being the important bit here.
When the Doctor swans into a crime scene, fast talks the guards and waves his psychic paper under their noses, it’s because questions of jurisdiction and other bureaucratic obstacles will tend to slow down an average episode. They can be fun when you get mired in a nightmarish dystopia of procedural excess, but less so when modern British procedures are concerned.
But a group that has to go through at least some of the proper channels may sometimes have to deal with such concerns. UNIT back in the day had to clear things with officials above, Torchwood had to get friendly-ish police on-side and avoid UNIT’s attention. And consider what the poor sods at The Laundry have to deal with.
A group like Skywatch would have an Oversight Committee, some of whom know what’s going on and some of whom have been sent from Parliament due to a cabinet reshuffle and would like to know why the programme is so expensive.
And for that matter, jurisdictional issues can get very messy if other departments start looking for aliens as well. In The Flood the Doctor is pressganged by MI6 (a clear influence on the attitude of Torchwood, among other things, in Army Of Ghosts) so what if another group formed by another branch of government turned up at the site of an alien incident? Or the police’s own paranormal experts? Or UNIT?
Something like this can really throw a spanner into a normal adventure.
Example: The Man From The Ministry
The team discover that they’re to be joined for the week by an observer from Whitehall. Just as a regular dangerous-use-of-alien-tech adventure starts off, they find themselves being followed around, asked lots of questions and recorded. The observer could be inept and prone to getting in the way, quietly competent, actually likeable, in service to a wider conspiracy, operating on a hidden agenda...