There are a huge number of stories set in the Doctor Who universe that don't feature the Doctor, far too many to count. Besides cases like "Mission to the Unknown" or "The Veiled Leopard" (audio story), the list includes (but is certainly not limited to):
- Most episodes of The Sarah Jane Adventures, Torchwood, and Class.
- Most episodes of most of Big Finish's spinoff audios series and miniseries, from Gallifrey to Jago & Litefoot.
- Some of the Companion Chronicles audios.
- Many of the backup comic strips in Doctor Who Magazine.
- Most of the in-universe-history articles from Doctor Who Magazine.
- Target's Turlough and Harry novels.
- Many short stories from Short Trips books, Doctor Who Magazine, and the BBC website.
And that's only counting stories that have licensed the entire Doctor Who universe; if you count those that have only licensed parts of it (the K9 TV series, the Bernice Summerfield novels, Terry Nation's Daleks books, the Kaldor City audios, the Autons home videos, etc.) there are even more.