The events of Jason X were a dream created by Freddy to test Jason.
Before using Jason to his advantage, Freddy wanted to know just what Jason was capable of. This explains both why Jason X was released before Freddy vs. Jason, and the ridiculousness of the premise. The opening of Jason X is set inside the S.C.P
After failing to execute Jason numerous times, he was picked up by the S.C.P foundation. No-one found him for years because the foundation chose to cut their losses after the breakout and seal off that part of the facility.