Threat levels were individual dungeons/stages that were analagous to "acts" in Sonic the Hedgehog games or "Stages" in Super Mario Titles. They were the shortest increment of gameplay from which one could get a reward Item, and could be chained together to increase the level of the item received. They were concluded by a "Horde" battle in a seperate arena, at the end of which the player must defeat a "Pit-Boss", if the stage ends in a -1, -2, or -3 and a Destructor if the stage ends in a -4. (Threat Levels were subdivided into "planets" similar to Zones or worlds in Sonic and Mario respectively; this was the first digit in a code, where the second digit represented the individual threat level. (I.E. Planet 2 Threat level 4 is 2-4). Difficulty Modes were fairly self-explanatory, in that depending on which one you played, the difficulty was adjusted; There were three, in ascending order of difficulty: Onslaught, Invasion, and Apocalypse.
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