The Doctor seen in The Continuing Adventures is a very changed man.
Allura McCoy and Mew are also very different than their canon selves.
Growing the Beard: The forum story Azumanga Randomness debuted the foul-mouthed Chrissie, a large backstory involving the "hospital era", a very stressed-out Allura (due to her daughter's changes, a growing hatred of the Doctor, and the natural stresses of running a legit hospital for 50 years), a series of events that brought forth the birth of Nanami and suggested that she had broken free of her time loop, indications that Susan Wise couldn't be stopped ever, and the First Doctor becoming free of the TARDIS' force field (which had prevented him from exiting the Ship because he became an anomaly after his thirteenth regeneration; long story) — basically, a great deal of the Continuing Adventures mythos was established here, spanning all parts of the author's continuity.
Tear Jerker: The Grand Eulogy. Written on February 22, 2010 (the day after his father's death) and published exactly two years later, the author dealt with the situation the only way he knew how: by talking to his characters. It also meant having to confront his father's parallel, Samuel Dleifneb.