The Doctor smiled gently at her. "It's not too much to ask, is it? I know a place where we can stay, one of the few places in the universe where I can really relax."
After so much chaos and drama, the Doctor has finally kept a promise to his companions and taken them on holiday. While he's messing around on trains, Nyssa and Tegan take advantage of a lazy morning idyll to bask in the glow of their new romance.
Then the box arrives. Before anyone knows it, Time and Space begin to twist as the intelligence within begins manipulating them for its own perverse entertainment until the Doctor is confronted with a future that technically speaking isn't his.
Something which can also be said for the son calling for his help, trying to win back his Independence...
"Confused? It's like we're stuck in a story where the plot is being written by eight different people who have no idea where it's going next, in what tense it's going to be written, or how to use proper grammar and spelling! Of course I'm confused."
Nyssa and Tegan have become lovers at some point following their reunion at the end of Arc of Infinity
The fifth Doctor's tooling around in a train comes from his remarking upon his fondness for steam trains in Black Orchid.
The humanoid TARDIS addressing the Doctor as 'father' has retroactively become the first appearance of Independence, who debuted in Not Even A Whisper.