故事发生在东京八丈岛近海,一座将全球各地警方监控相连接的高科技设施——“太平洋浮标”即将启动。为了与欧洲刑警组织管辖的范围联网,来自世界各地的工程师聚集在这里。基于人脸识别的全新“黑科技”也正在测试中……与此同时,柯南一行人前往八丈岛观鲸,途中柯南接到冲矢昴(赤井秀一)的电话,被告知欧洲刑警组织成员在德国遭到琴酒的杀害。为调查真相的柯南潜入“太平洋浮标”。正当工程师们正在为系统启动而展开准备工作时,一桩案件突然发生!一名女工程师被黑暗组织绑架,她手中存有核心技术的U盘也落入了黑暗组织手中!此时,水下传来未知潜水艇逼近的声音,令人毛骨悚然,一个神秘的黑影也正在悄悄接近灰原哀……
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