In 1999, Paramecium screwed Scott Thunder again. They were both in the middle of a tag title defense against Law & Order when Paramecium voluntarily laid down for the pin. Thunder was pissed and the feud was back on.
At Extravaganza 2 (the final PPV of the year) Scott Thunder challenged current World Champion Mr. Malicious to a title defense and won. He was now a three time champion.
In 2000, Scott Thunder once again fought his arch rival Paramecium - this time in the first ever Belt-in-the-Tree Match. The object of the match is to climb the tree, grab the belt and make it back to the ground with the belt in hand. Both competitors climbed the tree, grabbed the belt and jumped to the ground at the same time. But when the dust settled, Paramecium was the one left holding the belt. Paramecium had successfully ended Thunder's reign for the third time. A clause in the match said that there could be no re-match.
In 2002, Scott Thunder won the HaRdCoRe Championship becoming the first T.W.O. Triple Crown Champion - having held the World, HaRdCoRe and Tag Team Titles.
Scott Thunder and Paramecium once again joined forces as partners. Their mission was to rid the T.W.O. of the group known as Hell's Faction. The Faction gained control of both the Lighheavyweight and HaRdCoRe Titles and Thunder & Paramecium attempted in vain to prevent them from claiming the Tag Team Titles as well.