Expanded Universe History
In the Expanded Universe, a Jedi of Yoda's race confronted a Bpfasshi Dark Jedi on Dagobah some millennia before the events in The Empire Strikes Back. Eventually, the Jedi defeated the Dark Jedi, who died on Dagobah. The cave where the Dark Jedi died became strong in the dark side of the Force, and Yoda used this spot to hide from the Emperor and Darth Vader. This is a retcon of an earlier idea that Yoda himself slew a Dark Jedi there, causing the cave to become evil, since this explanation was contradicted by the canonical Clone Wars animated series, which portrayed Qui-Gon Jinn (via a flashback) taking the child Anakin to the cave to be tested, as Luke would later be, and the evil presence was there at that time as well.
However this is contradicted in the star wars film that Qui-Gon Jinn appeared in, where he first took Anakin to Coruscant, then took with him onto Naboo - there was no scene where he was shown to divert elsewhere during this time, or mention such a thing had happened. (This was all due to time being too critical to go on excursions that could be postponed). Nor could he have done this testing before he met Anakin, or after visiting Naboo with him, as he was cremated there after being killed by Darth Maul.
During the events of Star Wars Jedi Knight: Jedi Academy (for the PC), a team of Jedi Knights from the New Jedi Order visit Dagobah. However, it, like many other sites high in Force energy, has been drained in its dark Force power, leaving it less volatile and lush.
After the events of Episode VI, the New Republic founds a military base on one of the greatest mountains of the planet, named Mount Yoda in memory and in honor of the great Jedi Master.
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