The ship was flying through space, when the Doctor's TARDIS appeared on the ship's scanner. Although Gregor Van Baalen initially just saw it as 'junk', his brother Bram saw it as a chance to catch something. The ship's magno-grab was activated, which usually wouldn't have worked on the TARDIS due to it having shield oscillators, but the Eleventh Doctor had put the TARDIS into basic mode, leaving it vulnerable. After the TARDIS was brought on-board, the Van Baalen brothers broke in using cutting equipment to help the Doctor rescue Clara Oswald.
Later, after the Doctor reversed the timeline and created a new one, the TARDIS only appeared on the ship's scanner for a brief moment and was never captured. (TV: Journey to the Centre of the TARDIS)