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In this paper, we present a technological development of an autonomous underwater vehicle (AUV) docking system motivated by science requirements. Twenty-seven case studies were drafted after having elaborate discussions with twelve senior marine scientists from a wide range of oceanographic fields including physical oceanography, ocean chemistry, midwater ecology, biological oceanography, molecular biology, marine microbiology, geology, evolutionary biology, and benthic ecology. These science cases spread over coastal ocean, deep-ocean, mid-ocean ridge, and polar regions. All of these science missions can be significantly benefited from new and improved sets of data and samples that will be collected by using a docked AUV. The case studies are organized to address the science issue, significance of the problem, required data and measurements to address the scientific importance, a non-docked method for acquiring data, and the benefit of using a docked AUV. More than twenty science instruments (in addition to navigational sensors) are identified and evaluated for these science missions. Science pay loads for the AUV and the docking system are discussed in detail. Functional requirements for a general purpose docking system are identified and pros and cons of various docking subsystems are explained. A fuzzy logic based solution approach for an autonomous docking system design and development is also proposed in this paper.