He more or less had a long-term rivalry with Capcom's money-driven marketing for the Mega Man series, and this resulted in complete disregard to his wants, culminating in Mega Man X6-X8 and an altered plot to what Inafune had planned for the Mega Man Zero series. After more madness with the games and the production of Mega Man Legends 3, Inafune got up and left the company, which caused Ultimate Marvel vs. Capcom 3 to be what it is now, and caused the cancellation of Legends 3.
He launched a Kickstarter campaign for Mighty No. 9, a Spiritual Successor of Mega Man featuring a protagonist who can use Power Copying to transform himself. The Kickstarter was successful, but the game had a lot of Development Hell. He later launched another Kickstarter on the development for Red Ash, another Spiritual Successor, except for Mega Man Legends; though this campaign failed considerably, due to the delay of Mighty No. 9, the reveal that he was already funded by FUZE, and that a preview of Red Ash was poorly received.
Inafune maintains a working relationship with Inti Creates, a video game company itself comprised of ex-Capcom staff, which aided in the creation of the Mega Man Zero and Mega Man ZX series, as well as Mega Man 9, Mega Man 10, and the aforementioned Mighty No. 9. Their first self-published game, Azure Striker Gunvolt, was developed with Inafune's input and had additional cross-promotion for Mighty No. 9 in the form of Mighty Gunvolt, a free add-on title for those who downloaded Azure Striker Gunvolt by November 28, 2014. It features an imitation of 8-bit graphics (like the Mega Man a mini-game in ZX Advent) and Beck as a playable character alongside Gunvolt and Ekoro (of Gal*Gun, another Inti Creates title).
In mid-2017, Inafune's Comcept was bought out by the developer Level-5, and is now a subsidiary named Level-5 Comcept.