Disclaimer: I own nothing but my own OCs, should I create any for these stories.
Author's Note: Written for mindrobber on Teaspoon, who requested: "Something like how the Brigadier felt about having his Scientific Advisor just up and leave like that after Planet of the Spiders."
[This is actually set after Robot, when Four takes off with Sarah Jane and Harry, and makes brief references to Terror of the Zygons and the short story Hello, Goodbye, though no knowledge of the two is needed. This also marks my first (and probably only) concession to Four's era in this set of stories.]
It's been four days. Four days since the Doctor took off in his ridiculous TARDIS (with his medical officer, to boot), and already there's an invasion. At first, the Brigadier worries that they at UNIT won't be able to deprogram the aliens' weapons; not without his knowledge of technological wizardry, but as the battle rages on, it becomes increasingly apparent that he won't show up, and that UNIT is on their own.
The Brigadier makes himself a note to require that all the soldiers take some basic engineering and scientific courses after that.
Two weeks pass, and the Nestenes return to Earth yet again, attempting to subjugate the population. They try a different tactic this time; possessing children's toys in an effort to get Autons in everyone's home quickly. The Brigadier has to admit it's somewhat amusing to see grown men being pinned down by multitudes of small toy soldiers, but it's significantly less amusing when they're being physically overpowered by the larger waxwork versions of the same.
The Brigadier sends out a memo to Geneva detailing the importance of his men learning some forms of martial arts to assist in hand-to-hand combat shortly afterwards.
More weeks pass; spring turns into summer, and the Doctor still isn't back. At this point, UNIT is starting to run more efficiently on its own…at least, until the giant bumblebee people show up, literally crash-landing in UNIT's backyard. They call themselves the Menoptera, and they are a race of beings from the planet Vortis, caught up in a fight against another race they call the Zarbi. Regardless of how clearly they have stated that they are a peaceful race and wish the humans no harm, the Brigadier and Benton have to step in more than once to corral trigger-happy Privates and Corporals.
After this incident, the Brigadier himself leads a session for the entirety of the London HQ on the importance of listening to what alien races have to say before attempting to shoot them (if they aren't openly hostile, that is).
When the Doctor finally does return, it's been six months, and only because the Brigadier finally caves in and decides to make use of the space-time telegraph. It's clear that he doesn't want to be there; that he'd much rather be gallivanting all about the universe in his repaired TARDIS. He dismisses the problem as 'petty' and spends plenty of time making snide remarks about the Brigadier and humans in general, making the Brigadier wonder why he ever thought this was a good idea in the first place.
Soon, however, the problem is dealt with, and the Doctor rushes off again, leaving UNIT to clean up the mess. It's a familiar scenario, and yet, foreign at the same time - the Doctor hasn't gone back to HQ in that roadster of his to work on some new project, but off to some far-reaching time and/or locations to avoid the bureaucracy and paperwork that will invariably take place once the Brigadier has returned to the base.
Oddly enough, the Brigadier finds he doesn't mind the silence as he fills out the forms in triplicate; right now, anything is better than the cutting comments.
Another year goes by, and the Brigadier goes against his better judgement and uses the telegraph again; this time for a training exercise for new UNIT recruits. As he predicts, the Doctor is furious when he arrives on Earth, and no amount of reasoning on the Brigadier's part will make the wandering Time Lord agree to help him out. They argue for a good amount of time before the Doctor decides he's had enough and tenders his resignation, not wanting to be at the Brigadier's beck and call any longer.
Miss Smith tries to help; to mediate in some way, but the Brigadier is simply having too difficult a time reconciling this extremely mercurial version of the Doctor with his past self. Soon, however, his thoughts are interrupted by Benton, reporting fifteen alien craft over the Channel Island, and all thoughts of their argument flee from the Brigadier's mind as he begins to plan strategies to counter this potential attack.
He doesn't ask the Doctor for any help as he plans; having learned that UNIT needs to be able to stand on its own without leaning on the Time Lord's assistance. He's made sure that his men are more self-sufficient than they used to be, and taking some of the previous Doctor's principles and applying them to their organization they have helped tremendously in that regard. Over the past two years, he's been sure to teach all the men under his command a valuable lesson: they can't always rely on the Doctor to be there, because he won't be.
He doesn't notice when the Doctor leaves this time.