At the risk of becoming a creepy stalker, he’s been running into Donna a bit on purpose, more than once. They’ve met twice more in the bakery, once at the Castle, and once at the astronomy wing. It’s been grand, re-kindling their friendship, but he knows she’s wondering why he sometimes looks at her so sadly, even as he smiles.
Unbeknownst to her, but with a bit of help from her granddad (Good old Wilf, swiping Donna’s brush!) he’s gotten a sample of her DNA. Evaluation leads to the discovery that her DNA is still changing. That the regeneration energy has made hers look oddly like his. Not the slightly slowed aging, he doesn’t think, but there is definitely Time Lord in her very genes as well as locked in her mind. After his success with Jenny, he’s confident that if he can just get in her mind, he can sort it all out, bring her back without burning her brain.
Sitting on the steps, looking out at the Plass, he dials her mobile. “Donna! Hello! It’s John. Look, it’s a lovely day, and I’m at the Plass, you know, by the Millennium Center? Yes, that’s right. Anyway, I was wondering if you’d like to come…spend the afternoon with me? Maybe get some ice cream…” Once she says yes, he hangs up, looking around with a sigh. Once she remembers, she’s going to deck him for pretty much asking her on a date.