Scientific communities are straining under mounting challenges—knowledge fragmentation, outdated publication processes, institutional erosion and funding cuts that threaten our capacity to address urgent global problems. We propose Collective Augmented Intelligence for Research and Open Science (CAIROS) - a cooperative ecosystem supporting flourishing scientific communities through synergistic human-machine knowledge integration, participatory social networks for scientific discourse, and democratic stewardship. Through CAIROS, we envision a virtuous cycle where researchers’ contributions strengthen both AI capabilities and human collaborative capacity. Cooperative governance ensures accountability to scientific communities - transforming how knowledge is created, connected, and stewarded for flourishing science and society.