Existing methods for multi-agent navigation typically assume fully known environments, offering limited support for partially known scenarios with outdated or imperfect prior maps, such as warehouses or factory floors. There, agents need to balance path optimality with collecting and sharing environmental information to help teammates reach their own targets. To these ends, we propose ORION, a novel deep reinforcement learning framework for cooperative multi-agent online navigation in partially known environments. Starting from an imperfect prior map, ORION trains agents to make decentralized decisions, coordinate toward individual targets, and actively reduce task-relevant map uncertainty through online observation sharing in a closed perception-action loop. We first design a shared graph encoder that fuses prior map with online perception into a unified representation, providing robust state embeddings under environmental discrepancies. At the core of ORION is an option-critic framework that learns high-level cooperative modes translated into sequences of low-level actions, enabling adaptive switching between individual navigation and team-level exploration. We further introduce a dual-stage cooperation strategy that allows agents to assist teammates under map uncertainty, thereby reducing the overall makespan. Across extensive maze-like maps and large-scale warehouse environments, ORION achieves high-quality real-time decentralized cooperation while scaling to up to 10 robots, outperforming state-of-the-art classical and learning-based baselines. Finally, we validate ORION on physical robot teams, demonstrating its robustness and practicality for real-world cooperative navigation.