Sunspot regions often form complexes of activity that may live for several solar rotations, and represent a major component of the Sun's magnetic activity. It had been suggested that the close appearance of active regions in space and time might be related to common subsurface roots, or “nests” of activity. EUV images show that the active regions are magnetically connected in the corona, but subsurface connections have not been established. We investigate the subsurface structure and dynamics of a large complex of activity, NOAA 10987-10989, observed during the SOHO/MDI Dynamics run in March-April 2008, which was a part of the Whole Heliospheric Interval (WHI) campaign. The active regions in this complex appeared in a narrow latitudinal range, probably representing a subsurface toroidal flux tube. We use the MDI full-disk Dopplergrams to measure perturbations of travel times of acoustic waves traveling to various depths by using time-distance helioseismology, and obtain sound-speed and flow maps by inversion of the travel times. The subsurface flow maps show an interesting dynamics of decaying active regions with persistent shearing flows, which may be important for driving the flaring and CME activity, observed during the WHI campaign. Our analyses, including the seismic sound-speed inversion results and the distribution of deep-focus travel-time anomalies, gave indications of diverging roots of the magnetic structures, as could be expected from Ω-loop structures. However, no clear connection in the depth range of 0-48 Mm among the three active regions in this complex of activity was detected.