The plate tectonic history of the Junction Region, which separated the Panthalassa and Tethys realms, is notoriously challenging to reconstruct. The region has been dominated by intra-oceanic subduction zones, which has led to a sparsely preserved geological record because not only the down-going plates but also the overriding plates were lost to subduction. Even though most lithosphere that was present in the Junction Region during the Mesozoic has been lost to subduction, orogenic records preserve sparse geological data that provide information for a plate tectonic reconstruction. Here we present a kinematic reconstruction of the Junction Region back to the Jurassic, based on the present-day geological record of the circum-Philippine Sea Plate and Australasian regions, and sparse paleomagnetic data. We provide a comprehensive review of orogenic and oceanic architecture from Japan to the SW Pacific region and use a systematic reconstruction protocol for a plate kinematic restoration back to the Jurassic. Based on our reconstruction, we propose that the Molucca Sea Plate formed as an Eocene back-arc basin behind a north-dipping subduction zone that consumed Australian oceanic lithosphere. We find that the Jurassic oceanic lithosphere preserved in the Philippines originated from the northern Australian margin when a back-arc basin formed. By placing our reconstruction in mantle reference frames, we identify multiple cases of slab dragging and suggest that the lithospheric collapse that led to Izu-Bonin Mariana forearc extension may have been a trigger for the absolute plate motion change of the Pacific Plate that formed the Hawaii-Emperor Bend. Finally, we show that there is no need for spontaneous subduction initiation at the Izu-Bonin Mariana trench. Instead, subduction initiation was more likely forced through a change in Pacific-Australia relative plate motion around 62 Ma. Subduction started along a pre-existing Mesozoic subduction zone that had accommodated mostly transform motion since about 85 Ma. (c) 2023 The Author(s). Published by Elsevier B.V. on behalf of International Association for Gondwana