The Military Radar Jammer is a much higher power version of the Civilian Radar Jammer. It creates a lot more sensor interference and so is correspondingly much better at confusing the incoming missiles. This system has recently been tested against Auroran radar missiles and has shown itself to be enormously effective, but it has not yet been issued to all Federation capital ships.
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This system is normally not available unless you are working for the Federation military, but black-market systems occasionally show up for sale at some of the shadier outfitters. They are not quite as capable as a kosher Military Radar Jammer, but much better than the civilian version available at most outfitters. If you purchase one of these 'hot' items, however, don't be surprised if Federation patrol craft take sharp exception to your decision.