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General Alex Miles reports that the team disappeared while exploring an Underground Lake on Excelcion, and tasks the Federation Force with going there to find them. The Force reaches the lake and discovers the survey team's ship, and the team themselves alive. They battle two Sawkens and destroy the creatures.
The team reports evidence suggesting that the Space Pirates have been experimenting with augmentation technology, with the underground lake being their testing grounds. The Sawken creatures they encountered were native to the lake, but their size was unnaturally increased and the Pirates were able to control them. This is foreshadowing the final battle against Samus Aran, who is brainwashed and has her size increased via the amplification beam.