Amy and Rory have just about settled into their regular lives when once again the Doctor drops in for a visit. This time, it's because millions of little black cubes have popped up all over the planet. What are they made of? What's inside them? What's their purpose? Nobody can answer any of these questions. Even the Doctor is stumped. He hangs out with Amy and Rory while waiting for the cubes to do something, but soon becomes monumentally bored. He passes the time by taking Amy and Rory for a few quick adventures, while assigning Rory's dad Brian to cube watch.
A year goes by and the people of Earth have come to take the little cubes for granted. They use the cubes as toys, paperweights, or else ignore them entirely. That's when the cubes finally activate. Some of them shoot lasers. Others play music. Still others merely scan people. Each cube seems to do something different. This whole time, UNIT has been keeping an eye on things. The organization is now headed by the Brigadier's daughter Kate, who seeks the Doctor's help. After a brief, synchronized countdown, the cubes all over the world open and zap the nearest people. This causes heart attacks in a third of the world's population. The Doctor gets zapped, too, but luckily he's got that second heart to keep him going.
The Doctor tracks down the masterminds behind the cube plot. They are the Shakri, a people he had heretofore assumed were a myth. They are intergalactic pest controllers of a sort, and they've decided the human herd needed thinning. Or something. It seemed rather talky and boring and convoluted on first watch. The Doctor reverses the charges that zapped everyone and effectively defibrillates all the cube victims back to life.
Along the way, there's lots of the Doctor being preemptively sad about his coming goodbye with the Ponds, and lots of Amy and Rory trying to figure out which life they should choose. In the end, it's Brian who makes the most sense, telling them to have their adventures and save the world and so on, because how many chances like that do people get? Stay tuned for the full weecap.
Narrator Amy says, "Life with the Doctor was like this," and then there's hard rock music and flashes of all their crazy adventures. This contrasts this with her and Rory's everyday life, which consists of needing glasses and doing the laundry and cleaning out the fridge. They sit in the garden, chat, and realize they need to choose between their two lives. Right on cue, the TARDIS materializes and they decide they don't need to choose just quite yet. Narrator Amy says that although she and Rory became a part of the Doctor's life every time they left with him, he never stayed around long enough to become a part of theirs. This all changed during the year of the Slow Invasion, as she calls it. During her narration, a little black cube floats into her and Rory's bedroom and lands quietly on the nightstand.
The next morning, Rory's dad Brian shows up on their doorstep all in a tizzy. He's got a little black cube of his own. In fact, there are little black cubes dotting the sidewalks, windowsills and just about every other flat surface around. They establish that nobody knows what the little doohickeys are or from where they came. All Brian knows is that they seem to be everywhere. Amy notices the Doctor perched atop a playground structure nearby, studying one of the cubes. "Invasion of the very small cubes," he says, smiling. "That's new!"
Clips from news broadcasts around the world lend an air of verisimilitude. The best is from Professor Brian Cox, Star of those "Wonders of the Universe" shows and quite possibly the most adorable professor ever. "Well, they're certainly not random space debris," he says, holding up one of the cubes. "They're too perfectly formed for that. Are they extraterrestrial in origin? Well, you'll have to ask a better man than me." Not possible.
The Doctor and friends have gathered in the TARDIS. The Doctor says all the cubes are all identical, right down to their atoms. Brian worries they may be tiny bombs, or alien eggs, or parts of some awful jigsaw puzzle. Honestly, they look kind of like components for Ikea furniture. Like somewhere there's a giant alien who can't finish putting together his new media center because a bunch of the pieces got shipped to the wrong address. The Doctor, either impressed or humoring him, tasks Brian with watching over a stack of cubes. Meanwhile, the Doctor sets up a makeshift lab in Amy and Rory's kitchen to run a few tests. He's somewhat shocked to learn that Rory and Amy both have normal lives when they're not with him. While Rory gets ready for his job at the hospital, Amy says she thinks she and Rory have been traveling off and on with the Doctor for ten years. The Doctor notes, with both sadness and pride, that Amy's all grown up now. The tender moment is interrupted when armed UNIT soldiers barge into the kitchen. One of them marches a half-dressed Rory into the kitchen. "There are soldiers all over my house, and I'm in my pants," he says, gesturing to his cute little boxer briefs.