
On March 19, an anonymous employee reported to GameSpot that these changes were a result of conflicts between Kojima and Konami.

Speculation arose that Kojima had planned to leave Konami after the release of The Phantom Pain, which he had described as the conclusion to the Metal Gear series. That day, Kojima posted a photo on his personal Twitter account captioned "heading off", and a Konami filing stated that as of April 1, 2015, he would no longer be among Konami's executive officers. On March 16, 2015, Konami announced that it had restructured the game development operations to " our production structure to a headquarters-controlled system, in order to establish a steadfast operating base capable of responding to the rapid market changes that surround our digital entertainment business." Kojima and his company were stripped from promotional material and websites relating to the Metal Gear series, Kojima's Los Angeles studio was renamed Konami Los Angeles Studio, a new Metal Gear Solid Twitter account without references to Kojima in its username was established, and the Kojima Productions website began to redirect to the Metal Gear Solid website. The company produced two final video games for Konami, including Metal Gear Solid V: Ground Zeroes and Metal Gear Solid V: The Phantom Pain. They released Metal Gear Solid: Snake Eater 3D for Nintendo 3DS as a port for Metal Gear Solid 3: Snake Eater. The first Kojima Productions release was Metal Gear Solid HD Collection in 2011, a compilation of Metal Gear games. If they say, 'No! We don't know what you're talking about!' then this is actually the fun part."

According to Kojima, while he now held a position on the Konami board, he still had to persuade staff to invest in his game ideas: "That's my challenge, and my satisfaction when I present to them, saying I want to create this new thing. Kojima said the merger relieved him of business management and administrative burdens he had as KCEJ's vice president, and that as head of Kojima Productions he could focus on creating games.

Kojima Productions was formed on April 1, 2005, after Konami merged several subsidiaries including Kojima's team at Konami Computer Entertainment Japan. Kenichiro Imaizumi (producer), Yumi Kikuchi (model), and Hideo Kojima showcasing Metal Gear Solid 4 in 2007
