Apocalypse flasks are items found in Axiom Verge 2. Collecting these gives Indra skill points, which she can use to upgrade various skills and attributes such as health, damage, weapon speed, drone damage, drone weapon speed, hacking level, etc.
There are small and medium apocalypse flasks, each bestowing 1 and 2 skill points respectively. Despite the implication in their naming convention, there are no "large" apocalypse flasks in the game.
A small apocalypse flask.
Medium.