The Reference Desk/Information sought: Doctor's frenemy trapped in a separate universe

The text of the comic was not enough for me to figure out what it refers to:

An old friend of mine--well, enemy, really--once tried to create a new universe to rule maniacally--or something like that--I lost interest early into his monologue. I put a few minus symbols before his calculations, so it ended up a wee bit smaller than he planned. I've got it in my pocket. An entire universe all to himself, no other life-forms whatsoever. If you listen closely, you can hear him calling me all sorts of namesTwelfth Doctor tells this holding the universe in question between his thumb and index finger.

In the absence of proper names, I couldn't find this story. If it rings a bell for anyone, help is appreciated.