According to the episode transcript:
OSGOOD 1: Operation Double is a covert operation, outside of normal UNIT strictures, to resettle and rehouse an alien race in secrecy on planet Earth.
OSGOOD 2: With UNIT's help, twenty million Zygons have been allowed to take human form, been dispersed around the world, and are now living amongst us.
The Zygons are a dispossessed people. From the transcript of The Day of the Doctor:
ELIZABETH: The Zygons lost their own world. It burnt in the first days of the Time War. A new home is required.
CLARA: So they want this one.
ELIZABETH: Not yet. It's far too primitive. Zygons are used to a certain level of comfort.
The Zygon homeworld is gone, and as it's the result of the Time War, naturally, the Doctor feels some level of responsibility. So, working with UNIT, he uses the peace negotiations to include resettlement of some of the Zygons on Earth. Unlike races like the Daleks, Cybermen, or Sontarans, the Zygons are not -- by and large -- a warlike race, a few counterexamples notwithstanding. They are much more like the Silureans in that respect, just looking for a home.