Taught the shoot-style by Kazuo Yamazaki, who had returned to NJPW after leaving UWFI, Nagata learned the style that has been his trademark ever since.

The two rivals faced one another at Halloween Havoc on October 26, with Nagata forcing his smaller opponent to submit with an arm submission hold.

They faced one another in a rematch at World War 3 on November 23, with the added stipulation that, should Dragon win, he would receive five minutes alone in the ring with the interfering Onoo.

On September 23, 1998, Nagata fought Scott Norton for the vacant title (the previous champion, Masahiro Chono, had suffered a neck injury) in Yokohama, but was defeated.

On August 28, 1999, in Tokyo, Nagata and Manabu Nakanishi defeated Tatsutoshi Goto and Michiyoshi Ohara for the IWGP Tag Team Championship.

Fukuda died in April 2000 from a brain hemorrhage suffered during a match with rookie Katsuyori Shibata, and was honored with a ten-bell salute and a tribute show in September of that year.

Nagata challenged for the IWGP Heavyweight Championship once again after it was vacated by the injured Kazuyuki Fujita on January 4, 2002, but lost to Tadao Yasuda on February 16, 2002, in a tournament final.

In the fall of 2009 Nagata formed the stable Seigigun ("Blue Justice Army") with Wataru Inoue, Mitsuhide Hirasawa and Super Strong Machine.

Yuji had started mentoring both Inoue & Hirasawa, and Strong Machine was entering the role of head trainer at New Japan's dojo.

On May 3, 2010, at Wrestling Dontaku 2010 Nagata and Wataru Inoue defeated No Limit (Tetsuya Naito and Yujiro Takahashi) and Bad Intentions (Giant Bernard and Karl Anderson) in a three-way match to win the IWGP Tag Team Championship.

[7] On June 19 at Dominion 6.19, Nagata and Inoue lost the Tag Team Championship to Bernard and Anderson in a three-way elimination match, which also included No Limit.

[8] In September Mitsushide Hirasawa left for a learning excursion to Puerto Rico and his spot in Seigigun was given to newcomer King Fale, who was also trained by Nagata & Strong Machine.

[11] After four wins and a loss, Nagata and Inoue won their block and advanced to the semifinals of the tournament, where, on November 7, they defeated the IWGP Tag Team Champions, Giant Bernard and Karl Anderson.

[13] As a result of their victory, Nagata and Inoue received a shot at the IWGP Tag Team Championship on December 11, 2010, but were defeated by the defending champions, Bad Intentions.

[22] On June 18, Seigigun member Mitsuhide Hirasawa, now working under the ring name Hideo Saito, returned from his Puerto Rican excursion, turning on Nagata and joining Chaos.

[25] On September 19, Nagata seemingly wrapped up his rivalry with Saito by defeating him in a singles match, but was then attacked by his CHAOS stablemate, Toru Yano.

[34] From November 20 to December 1, Nagata and Mochizuki took part in the round-robin portion of the 2012 World Tag League, finishing with a record of four wins and two losses, narrowly missing advancing to the semifinals of the tournament.

[53] Nagata started his 2015 without a match on the January 4 Tokyo Dome show, but he won the pre-show's New Japan Rumble, pinning Yoshi-Hashi with a Backdrop Driver to win.

[54] The next night, Nagata again pinned Yoshi-Hashi in a six-man tag team match featuring IWGP Intercontinental Champion, Shinsuke Nakamura.

[55] On February 14, 2015, Nagata returned to the singles title picture in his home promotion, when he unsuccessfully challenged Nakamura for the IWGP Intercontinental Championship at The New Beginning in Sendai.

[60] Nagata was again in the New Japan Rumble on Wrestle Kingdom 10 in Tokyo Dome's pre-show, but he was unsuccessful this time, being eliminated by King Haku.

On May 3, 2016, at Wrestling Dontaku 2016, Nagata won his first NJPW singles title in nine years, when he defeated Katsuyori Shibata for the NEVER Openweight Championship.

He again competed in the New Japan Rumble at Wrestle Kingdom 12, this time eliminated by Nakanishi, Chase Owens & Katsuya Kitamura all at once.

[80] On February 3, Nagata and Jun Akiyama defeated Naoya Nomura & Ryoji Sai to win the All Asia Tag Team Championship at All Japan Pro-Wrestling's Yokohama Twilight Blues Special.

The duo first defended against a reunited 'Wild Child' (Nakanishi & Takao Omori) on March 25, and then against 'Nextream' (Naoya Nomura & Yuma Aoyagi) on June 12.

[88] At Wrestle Kingdom 14 in Tokyo Dome, Nagata was again on the pre-show, this time in a tag team match alongside Nakanishi to take on Tencozy, which they lost.

!, Nagata defeated Young Lion, Gabriel Kidd via submission in 7 minutes and 59 seconds with the 'Nagata Lock II' (Arm-Trap Crossface).

[97] In the leadup to Resurgence, Jon Moxley teased that he would be joined by a mystery tag team partner in his match against The Good Brothers.

[100] On September 21, Tetsuya Naito was forced to withdraw from the G1 Climax 31 due to a knee injury suffered during his match with Zack Saber Junior.

[103][104] As a result of his Global League win, Nagata received a shot at the GHC Heavyweight Championship, but was defeated by the defending champion, Kenta, on December 7.