The Doctor locks himself into one of the isolation chambers with a cube, for reasons I'm not entirely clear on. A lot of time is spent watching the cubes finish their countdown. The little girl in the waiting room waits. Finally, the cubes open. "Geronimo," says the Doctor. He peers inside and discovers... nothing. He's confused and pissed. Video feeds all over the world show people dropping dead. The Doctor starts his usual "talk to himself until he figures things out" thing but then crumples to the floor in pain. He's having an attack in one of his hearts. He flails and mugs like he drew "Jim Carrey" in a game of charades. His other heart's still working, so he blathers on about the cubes' evil plan to destroy humanity by targeting people's hearts. Anyone who was near a box got zapped. A scan of the planet turns up a transmitter on each continent. "Seven stations, seven minutes. Why is that important?" asks the Doctor between flailings. They see that the closest transmitter is at the hospital where Rory works.
Rory passes through the portal onto the ship. He lands in a spacious area that would make a great observation deck if it were open to tourists. All the nice windows overlooking space. Rory sees his dad lying unconscious on the gurney. Other people are in a similar state, although lying on marble platforms. The PTs approach Rory with syringes.
The Doctor, Kate and Amy make their way through the hospital. "How many deaths have been recorded?" the Doctor asks. "We don't know; we think it could be a third of the population," Kate says. Professor Brian Cox better be okay, damn it. While Kate and a handful of UNIT soldiers go off to do... something... the Doctor and Amy go in search of the wormhole that the Doctor's sure is there. He waves the sonic screwdriver around while Amy holds him up. He finds the little girl with the freaky blue eyes. "Hello! You are giving off some very strange signals," the Doctor says. Her whole face glows blue. The Doctor scans her and announces: "Outlier droid, monitoring everything." Um... okay. He shuts her down. He flails about some more, so Amy grabs a nearby defibrillator, rips open his shirt and gives him a zap, all while he protests that it won't work. It does work, and he hops up to start dancing around like he's got a bad case of Saturday Night Fever.
Eventually he remembers they've got other things to do and they work their way to the elevator. The portal shimmers. He and Amy exchange excited grins. It's not like a third of the planet is dead or dying or anything. Take your time and enjoy the adventure! They clasp hands and jump through the portal.