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A bio-molecular warhead was a specially-modified photon torpedo utilized as a delivery-system for Borg nanoprobes with which to combat Species 8472. Designed in 2374 by the crew of the USS Voyager in collaboration with the Borg Collective, the warheads contained a series of nanoprobes modified by The Doctor to attack 8472 on a microscopic level, constituting a weapon which could not be replicated by the Borg, necessitating an alliance.

The crew constructed thirteen warheads using standard class-6 photon torpedoes, and one class-10 armed with a high-yield warhead. Entering fluidic space, Species 8472's native realm, Voyager engaged in combat with four bio-ships, successfully destroying them with the warheads. Voyager was subsequently pursued by 8472 back into normal space, where the Voyager crew utilized the high-yield warhead, destroying thirteen bio-ships, and prompting 8472 to retreat to fluidic space. (VOY: "Scorpion, Part II")

A year later, as a sign of good faith, Captain Janeway agreed to share Voyager's nanoprobe technology with Species 8472 in exchange for tactical information. (VOY: "In the Flesh")

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