Terror of the Zygons also features Brigadier Alistair Gordon Lethbridge-Stewart, father of Kate Stewart featured in The Power of Three. Like her dad, Kate works for UNIT (Unified Intelligence Taskforce), which is now stationed under the Tower of London. UNIT is basically the military response to extraterrestrial shenanigans - they tend to point guns at whatever's invading Earth at the moment. UNIT has plenty of history with Doctor Who, as well as its spin offs The Sarah Jane Adventures and Torchwood. When you need a discreet army - or at least as discreet as an army can be with rocket launchers and tanks - UNIT are the folks you want.
The Doctor has long had a relationship with UNIT, most prominently when the Time Lords exiled the Doctor on Earth, which is when he formed his lasting bond with Brigadier Lethbridge-Stewart. We learn in Mawdryn Undead (1983) that the Brigadier left UNIT to teach mathematics at a boy's school - the same school where we met Turlough, the alien who made a deal with the Black Guardian to kill the Doctor in return for a way off Earth. (That's also the episode where we discover what happens when you cross your own timeline and meet yourself. As the Doctor puts it at the time, "ZAP!") The Brigadier never actually appeared in New Who, but was mentioned many times, until finally, in The Wedding of River Song (2011), the Doctor learned that he had passed away.
Kate gets involved as UNIT tries to determine the level of threat the cubes present. They don't seem to be doing anything, but there are billions of them scattered all over the world, and they seem to be completely invulnerable. The Doctor decides to wait around at Chez Pond until the cubes fulfill their purpose, whatever it may be. He also goes a bit bonkers as he waits, and takes to mowing the lawn, painting the fence, and playing lots of Wii Tennis. Eventually, each cube does something different - gushing fire, taking a blood sample, causing mood swings - as they simultaneously learn everything there is to know about humanity. They then begin counting down from 7 for no really sound reason other than to make me want a black clock that displays the time in the same luminescent blue as the countdown digits. (Tell me that wouldn't look amazing on my desk.) When the countdown stops, about a third of the world's population gets zapped and has a heart attack. Boom.
The cubes turn out to be a tool of the Shakri, a sort of intergalactic pest control service that's looking to thin out humanity before we infest the rest of the universe. The cubes provided intel on the best way to take us out, finally settling on using electricity to disrupt our hearts. I'm not entirely sure why it took so long - one season of any medical drama will tell you out how fragile the human heart is. But a wave or two of the sonic screwdriver and the Doctor has given everyone a reverse zap on the old ticker, blown up the Shakri ships and whisked Amy and Rory back to Earth.
The slow invasion was moderately cute, even if it did crib rather a bit from Army of Ghosts (2006), though the resolution did feel quite rushed. There were some nice nods to the lore, and a few good laughs, but I couldn't help feeling like this episode only existed to tell us what we already knew: The Doctor's relationship with Amy and Rory is special, and it is ending. The biggest red flag was when the Doctor admitted to Brian that some of his previous companions had died, but never, never would that happen to the Ponds. As foreshadowing goes, it's a bit heavy handed, but there's not much else for these two go through.
Well, we'll find out soon enough, when The Angels Take Manhattan. (Hmm ... Manhattan, eh? Think we'll run into any Daleks?)