Flares are cards that cause various effects when played. Each alien has a corresponding flare card; during setup, the flares corresponding to the alien powers that are in play, and an equal number of flares corresponding to aliens not in the game, are shuffled into the deck before starting hands are dealt. There are two effects on each flare: Wild and Super. If the player's alien power does not match the alien named on the flare card, or if it does but the player's power is lost, the player can only use the flare's Wild effect. But if it matches and the player has his or her power, the Super effect is used instead.
In most editions of Cosmic Encounter, flares return to their player's hand after being played. In the current edition, each player may only play one flare per encounter and each flare may only be played once per encounter.