River appears in Episode Thirteen, just after the events of Flesh and StoneRiver Song appears in camouflage gear, and Amy and her cross check their diaries. River says she’s just climbed out of the Byzantium, "you were so young, didn’t have a clue who I was", she says to Amy.

She asks Amy where she is in the timeline, and she says the Doctor is dead and that she’s sad. Not just because of that, because she killed Madame Kovarian. River says it’s fine, it was in an aborted time-line, so never happened. But it still happened for Amy, she remembers it.

Amy longs to see her Doctor again, but she can’t, he’s dead. River then says "Oh mother, he isn’t dead, don’t you want to know what he whispered in my ear?". Amy assumes it was his name. River says no it wasn’t his name. Amy says that the Doctor said he was about to whisper his name to River, but he clearly didn’t. He whispered something to stop the astronaut killing him.
River reminds Amy about rule number one. The Doctor lies. So do I, she says. River says her life is one giant spoiler. She’s had to keep it from Amy that she’s her daughter, and keep secret about the astronaut: she knew all along it was going to shoot the Doctor. So Amy pushes her to say what the Doctor whispered in her ear before he went off to America to get shot. River grins and says "that man, always thinking so far ahead".

The same poster goes on to tell us that River did do enough to earn that pardon in Flesh and Stone, and sees Amy after she is released from Stormcage. He also mentions that River is married to The Doctor.