The Shakri ship was used by the specific holographic image of a Shakri. It was used to deposit small black Shakri cubes on the Earth's surface in order to learn about humans, and later kill them by inducing cardiac arrest in anyone within range.
The ship was connected to Earth using wormhole portals from seven different places on Earth. It was "one dimension to the left". The Eleventh Doctor and his companions Amy Pond and Rory Williams used the one closest to them in London, which was hidden inside a disused lift.
This ship was destroyed as a side effect of the Doctor using the cubes to revive all the humans who had suffered cardiac arrest. The Doctor created a giant energy wave, producing a form of mass defibrillation which would restart all the stopped hearts onset from the cubes. However, the wave ricocheted in the direction of the Shakri ship and blew it apart. (TV: The Power of Three)