A/N: I know this kind of doesn't fit with the canon timelines but it really doesn't matter that much to be honest.
Disclaimer: I do not own anything you recognise
The first sign that something was very wrong happened to be the fact that the Doctor had simply acknowledged Jack's unexpected presence on the TARDIS without any fuss or surprise, even though they hadn't seen each other since Martha was still travelling aboard. The second sign was the completely uncharacteristic silence from the obviously upset Time Lord. The third and most worrying sign was when Jack looked over at the Doctor and noticed that he was struggling to hold back tears.
Extremely worried for his closest friend and target of his unrequited infatuation, Jack had ushered Donna to a place in the TARDIS where the Doctor would not overhear their conversation and asked her what had happened to make the Doctor so distraught.
"He just finished Harry Potter and the Deathly Hallows."