In March and April 2003, the Chandra X-ray Observatory carried out a series of 126 short observations (5 ksec each) covering a continuous area of the Bootes constellation to construct a large area shallow X-ray survey. These observations were carried out as collaboration of Guest Observer (C. Jones PI) and Guaranteed Time Observer (S. Murray PI) programs. We present here, in Paper I, an initial analysis of the survey data and the source detection process, showing the sky coverage, exposure map, and some of the collective properties of the resulting catalog of sources. The Bo\"otes area was selected to overlap a well studied region where optical, and radio data, to sufficient depth, have already been obtained making the identification of candidate counterparts straight forward. In 5 ksec, we reach a limiting flux of ≈10-3ct s-1 (corresponding to ≈10-14 erg cm-2s-10.5-7.0 keV). We examine the spatial distribution of the sources in this ~9.3 square degree survey region using several techniques to search for evidence of cosmic variance in the X-ray source density on scales as small as the ACIS-I field of view (~16x16 arc minutes). With follow up optical spectroscopy using the MMT/Hectospec, we can obtain spectroscopic redshifts for about 1/3 - 1./2 of the X-ray sources, which can be used to look for evidence of large scale structures traced by AGN associated with the cosmic web.