Courtney looks down and realises that her hands are glowing, it turns out that the master planned this from the start, he planned to use Courtney to get back at the doctor.
It was too late for the doctor to do anything to save his daughter, he was just compelled to watch his daughter change before his eyes, he slowly made his way towards the master around Courtney who was currently changing in front of him.
The regeneration progress has finished, Courtney falls down , everyone who witnessed court justed regenerated rushed towards her, the doctor has reached the master finally going to defeat him while both of them are on Gallifrey for the last time.
Court notices that her dad and the master are preparing to battle once again she attempts to stand up and she tries to say "dad its a trap like last time like last time don't you remember he framed you for the murder of the president but this time he found a way round to defeat you though me, he knew all this time that you've got a daughter, he is using that knowledge to use that against you, he was close to do so but he is going to fail again this time round again."
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The Doctors Daughter
Ciencia FicciónThis is how the doctor realised that he's got a daughter (4th specially) This is not canon to the doctor who Franchise