On January 4, 2012, Funaki made a special appearance for New Japan at Wrestle Kingdom VI in Tokyo Dome, where he teamed with Masayuki Kono to defeat the Seigigun team of Yuji Nagata and Wataru Inoue. During the match, Nagata broke Funaki's orbital bone, sidelining him from in-ring action for an estimated six months. Funaki returned to the ring on June 17, 2012. On July 29, he defeated the man who had injured him, Yuji Nagata, in a grudge match to become the number one contender to the Triple Crown Heavyweight Championship. On August 26 he defeated Jun Akiyama in a match that lasted less than five minutes to become the 45th Triple Crown Heavyweight Champion. He lost the title to Suwama on March 17, 2013. In June 2013, Funaki announced his resignation from All Japan in the aftermath of Nobuo Shiraishi taking over as the new president and Keiji Mutoh leaving the promotion. Funaki's final match for the promotion took place on June 30 and saw him and his Stack of Arms partners Koji Kanemoto and Masayuki Kono, who were also leaving All Japan, lose to Akebono, Osamu Nishimura and Ryota Hama in a six-man tag team match.