The Nameless City (Doctor Who 50th Anniversary E-Shorts, #2)
Well, that's more like it. I had the same problem with this one that I had with the last one, in that I'm not really all that familiar with the Second Doctor, but in terms of the actual story itself (the villains, the plot, the writing, the atmosphere, etc), Michael Scott's venture into the world of Doctor Who seems to me to be the superior offering. He also seems to have gotten his version of the Doctor's world to a more consistent place than Colfer did, what with Colfer's strange references to Harry Potter and such (yes, technically the First Doctor would have known about it, but it didn't feel true to the spirit of that version of the character).
This one brings back The Master (in disguise as Professor Thascalos) and the Archons, who I'm hoping will eventually make an appearance in the new series one of these days. I also really liked Jamie as the Doctor's companion. Refreshing to have a dude after so many of New Who's young nubiles (not that I'm complaining, because I love Rose and Martha and Amy and Rory, but Donna is my favorite companion and she can't really be considered young or nubile, and Jack and Wilf were great, too).