After losing to the Power Warrior on January 4th, 1997, the Great Muta was soon invited to join the nWo. The nWo, lead by Hulk Hogan, Kevin Nash, and Scott Hall in WCW, had taken the wrestling world by storm in America and was now spreading to Japan. Chono was the leader of nWo Japan and invited Great Muta to take part. At first Muta declined, but on April 12th, 1997 he finally accepted. Curiously, Mutoh didn't join the nWo, only Great Muta, so Mutoh still wrestled for the regular army. During all this, Mutoh got another shot against Hashimoto for the IWGP Heavyweight Championship in June but Hashimoto once again was too much for Mutoh to defeat. For the first time, it was nWo Great Muta that wrestled in the G1 Climax that summer, but he lost in the Quarter Finals. On September 23rd, 1997, Mutoh joined the nWo as well, and a month later he would team with Chono to win the IWGP Heavyweight Tag Team Championship for the fifth time. With Mutoh joining the nWo, for the first time he started wrestling in long black tights instead of his red trunks, and he grew a scruffy beard to show his departure from the regular army.

In 1998, Mutoh's penchant for moonsaults finally caught up with him, as he was on the shelf when the year started due to knee injuries. It would be the first significant amount of time he had missed in his 15 year career up to that point, and it forced him and Chono to vacate the IWGP Heavyweight Tag Team Championship. His knees still in bad shape, he lost in the first round of the G1 Climax and it appeared that Mutoh's time as a top level performer were coming to a close. But after Chono's injury, Mutoh took over as the head of nWo Japan and he led his group until Chono recovered. In December, Mutoh teamed with Kojima (who he was trying to recruit into the nWo) and they won the G1 Tag League, making it the fourth time that Mutoh won the tournament (he also won it in 1997, teaming with Chono). As Mutoh lead the nWo, he became more negative toward the former leader Masahiro Chono, and it was clear that the two would clash once Chono recovered from his injuries.

On January 4th, 1999 at the Tokyo Dome, Keiji Mutoh challenged Scott Norton for the IWGP Heavyweight Championship and shocked many when he won the match to win the title for the 3rd time. Having a resurgence after many years behind Hashimoto in the pecking order, Mutoh held the title for the entire year, defeating Kensuke Sasaki, Don Frye, Genichiro Tenryu, Satoshi Kojima, and Manabu Nakanishi along the way. He also came in 2nd Place in the G1 Climax, his best finish since winning it in 1995. But as predicted, a power struggle took place after Chono returned, and Chono formed T2000 to counter Mutoh's nWo, taking some members with him. A massive nWo Japan vs. TEAM 2000 feud began, with it coming to a head at the Tokyo Dome on January 4th, 2000. A singles match between Mutoh and Chono was set to settle the score, with the stipulation being the loser had to disband his team. Chono would win the match, and nWo Japan was over. After losing to Chono and Sasaki in consecutive months, in August the Great Muta returned to WCW for a quick run. Teaming with Vampiro, the Great Muta won the WCW Heavyweight Tag Team Championship (even though they lost it the next day). The Great Muta's last appearance in WCW as at Fall Brawl, where he would fall in a three way match against Sting and Vampiro. Suffering from continued leg injuries, Mutoh went on hiatus after this, with his future unknown.

Throughout his career, one of the main reasons Mutoh stayed successful was his ability to adapt. In one of his best career decisions, in December of 2000 at Inoki's "Bom-ba-ye" New Year's End event, Mutoh returned but not as people remembered him, but completely bald and wrestling a more strike-oriented mat based style. Due to his knee injuries he transitioned away from doing the moonsaults and in the process created a new finisher that would be used by countless other wrestlers over the years: The Shining Wizard. Mutoh had succcessfully re-invented himself, and he instantly found success in the ring. After winning both his Tokyo Dome matches in January (one in New Japan, one in All Japan), Mutoh defeated Toshiaki Kawada for the first time in April. Mutoh became the leader in the feud against All Japan, and on June 8th, 2001 he invaded All Japan and became the first New Japan contracted wrestler to ever win the All Japan Triple Crown! Mutoh held the title for the rest of the year, defending it in both promotions. During this period he also created a new faction: Bad Ass Translate Trading (BATT). The faction had wrestlers from different promotions, with Taiyo Kea, Jinsei Shinsaki, and Hiroshi Hase joining him in his matches in both All Japan and New Japan. Already with three belts around his waist, Mutoh wasn't done, and on October 22nd, 2001 he teamed with Kea to win the All Japan World Tag Team Championship. Still not done, just a week later they challenged for the IWGP Heavyweight Tag Team Championship, and again they would come out victorious, making them the first team to ever hold both titles at the same time. They participated in the World World Tag League as well, winning that also, cementing them not only as the top tag team in Japan at the time, but one of the must successful teams in puroresu history. 2001 was an amazing year for Mutoh, as in one year he went from pondering what to do next, to ending the year with six championship titles around his waist (and shoulders). But 2001 was nothing compared to the changes that would take place in 2002, a change that would have a permanent effect on puroresu.

Go to 2002-2008: The All Japan Era