Rogue
He goes by Tempest, but no one knows his true name.
They have a rather cliche goal: world domination. However, their methods are much different than previous teams. They stay hidden and do small but effective strikes instead of large public sieges. They aim to achieve these goals by installing agents in positions of power. Tempest, for example, is on the path to becoming the champion, however under an alternate pseudonym. Rogue is particularly brutal and are not afraid to kill and destroy. They have already committed multiple assassinations of high ranking officials and planted bombs in several important buildings. They go in at night, accomplish their mission, then destroy the building the next day, removing all evidence. Officials know these operations where all done by one organization, but have almost no intelligence beyond that. They aren't planning to capture any legendary Pokemon, but if the need arises, they have the capabilities to do so.
Grunts or Agents as they are called, are few in number, as the organization is relatively small, but still very capable trainers. They tend to use darker and more sinister Pokemon, but still have balanced teams. They tend to have three to four Pokemon.
Leaders or the Four Shadows as they are called, and black agents use the same kind of team as the Agents.
Tempest
The teams rank structure is Tempest as the leader, then the Four Shadows, black agents and then agents. There are ten black agents and they command over the agents and receive orders from the Four Shadows. They run they're own missions but they are smaller and not as important compared to the ones run by Tempest and the Shadows.
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Obviously this is meant for a very difficult game as even the agents use powerful Pokemon and most run competitively viable teams.