Geopolitical conflict poses significant challenges to research and innovation policy by disrupting scientific systems and talent mobility. This study analyzes the impact of the conflict between Russia and Ukraine, particularly the escalations in 2014 and 2022, on the academic landscapes of both countries. We analyzed publication data from 2000 to 2023, encompassing over 1.8 million papers, one million scholars, and 2300 institutions across Ukraine and Russia, alongside collaboration data spanning 193 regions. We tracked scholar migration, research topics, and evolving international networks. Significant migration followed the 2014 and 2022 events, causing severe talent loss and a sharp decline in domestic research visibility in Ukraine. Migrated Ukrainian scholars shifted toward internationalized basic sciences, whereas active scholars who remained focused on applied fields relevant to national resilience and reconstruction. Both groups experienced decreased output in resource dependent fields, particularly medical research. Global networks fractured: traditional ties between Russia and the West, as well as between Ukraine and Russia, dissolved. These were replaced by new alignments between Russia and neighboring countries, and between Ukraine and the West. Migrating Ukrainian scholars face challenges assuming key research roles, though academic communities in smaller host nations showed a trend toward leadership positions. Concurrently, Russian scholars saw a decline in research prominence across most countries due to international sanctions. These findings reveal how conflict disrupts national scientific capacity, fractures global research networks, and affects individual academic careers, highlighting the need for targeted policies to support vulnerable academic communities during crises.