I am adding my own "telling Brian about the Ponds" story to the pile. Spoilers for the gut-wrenching sob-fest that was "The Angels in Manhattan". Moffat, you're a jerk.
Exactly two years, three months, and sixteen days after they leave, Brian Williams stops watering their plants.
In fact, he stops going to their house altogether. Phone calls to their mobiles are useless and he wasn't entirely sure about the TARDIS having a phone number. Maybe it did, but he certainly didn't have it. Instead, he busies himself with the upkeep of his own house and his job.
The days and months pass sluggishly without a word. Diving for the phone whenever it happens to ring only gets him bruises in places that bruises are definitely not supposed to be. Nevertheless, he always carries the mobile that Rory insisted he buy for emergencies.
On the day after the three year mark, upon arriving back home after a quick drive by their still-empty house, Brian pulls his car into the driveway. Making his way to the front door of his house, he notices that the front door is open. It hasn't been pried open, but instead either picked or gotten into by someone with the key.
Overcoming his self-preservation instincts with a surge of hope, he rushes up the steps into the house, hollering at the top of his lungs. "Hello? Hello? Is someone here? Amy, Rory?"
He pauses, hearing an odd noise, almost like- "The kettle's boiling?" He makes his way into the kitchen through the living room, past a coffee table and a worn sofa, where a woman with ridiculously curly hair is tending to the kettle and two cups of steaming hot tea.
River raises her head and gives him a smile. "Hope you don't mind. It's been such a long time since I had a good cuppa."
"Wha- Who are you? What are you doing in my house?" Brian attempts to puff himself up, but the woman only smiles wider.
"No need for that, Brian. Here," she says, handing him his cup. "Let's go into the dining room. I have something I need to tell you."
Brian follows her, wondering just how this woman knew his name. He takes his normal seat at the table and she sits to his right, sipping at her tea. He ignores his completely. "How did you get in my house?"
She only smiles mischievously and flashes her wrist. "Vortex manipulator. Time travel that's a bit more reliable than the TARDIS."
Brian feels his heart swell with a second wave of hope. "Is it about Amy and Rory? Where are they, are they alright?"
River takes a moment to mentally prepare herself. It hasn't been long for her. She travelled with the Doctor for a spell, then decided to return to teaching for a while, but only after doing this one last thing. "Amy and Rory... They-"
"Died. Didn't they?" he whispers.
River purses her lips together. God, the look on his face. It would be enough to send any less prepared person into a fit. "Yes. Yes they did. But they died together, of old age if you can believe it."
"Old age? How old?"
"Rory was 82. Amy lived to see 87. They were attacked by something called a Weeping Angel." She explains what exactly the Weeping Angels did and why going back for his son and daughter-in-law was impossible.
"But they lived."
"Yes, they did. And they were very happy together."
"Good," he says, rubbing his eyes. "That's a weight off my mind. I've been waiting and going to the house and-"
River reaches up and runs her thumb across his cheek, brushing away the tears that are spilling from his eyes. "I have something else to tell you as well. Something much happier."
"W-what's that?" he chokes out, reaching to accept her offered handkerchief.
"While Amy and Rory were traveling with the Doctor, Amy got pregnant."
Brian stares at her. "A baby? I have a grandbaby?"
River smiles at his enthusiasm. "Yes. She had a baby. A little girl named Melody."
"Melody... That's funny. Rory had a little friend named Melody once. Only they called her Mels."
"I know," River says, eyes sparkling with mischief. "Melody was... taken from Amy and Rory. Kidnapped and taken far, far away. They never got to raise her or see her grow up. Except they did." Brian is confused and opens his mouth to speak, but River hushes him and continues. "Mels was their daughter. She was taken through time and space, but she found them. She grew up alongside them."
"Wait a minute, how is that possible? Mels' skin colour-"
River holds up a hand to silence him and he promptly shuts his lips. "Melody is a special baby. Conceived in the TARDIS, she is half human and half Time Lord. The Doctor is a Time Lord as well, with the ability to remake his body when he is dying. It's called regeneration and Mels could do it too. She regenerated into a child to grow up beside her parents."
"I see... sort of," he admits. "Where is she now? And how do you know all this? Are you...?" He pauses, ignoring the math in his head. Since time travel was involved, ages and years passed were irrelevant. "Are you my granddaughter?"
"Yes," she says, pleased he was able to figure it out himself, though she never doubted him for a second. "I am Melody."
"You're... all grown up!" he says in wonder, reaching for her hand and grasping it in his own.
River chuckles. "Yes. But I remember you when I was a kid. You never called me Mels," she says, shaking a free finger at him. "Always Melody. But I go by River now, for a few reasons."
"River... Nope, I like Melody better," he says stubbornly and they laugh.
A few hours later, the two stand outside Brian's home to bid each other farewell. "What will you do now? Will you come back and visit your old Gramps sometimes?"
"I'll try," she says, not promising anything. "I work as a professor at a university, so I don't always have time of my own."
"Ah... Luna University. It's on the moon," she explains, pointing upward. He looks both bewildered and excited at the prospect of a school on the moon.
"I hope to see you again, Melody," he says, drawing her into a hug. "If you see the Doctor, tell him... Tell him I'm not angry. Please?"
"Oh, I will. I promise. I should see him soon, he'd better remember our anniversary," she adds, half to herself.
"Anniver- Are you married to the Doctor?!" He bursts out laughing. "Then I'd better see some great-grandbabies!" He gives her a wink and she only grins in response.
"Goodbye, Granddad. I'll see you again, I hope." River types the coordinates for Luna University into her vortex manipulator and disappears, leaving Brian Williams to mull over all he has learned.