NOAH was in such bad shape that in 2015 New Japan came in and put some money so they could have a minority share. They sent Jado (who at the time was still booking New Japan along with Gedo, or at least was coming off helping with the booking of NJ for a long time) to be the booker, pay for some gaijin and sent Suzuki Gun to inject new talent and feuds to the company. Super Crazy, who was working with NOAH during those days, said in an interview the idea was to make it "New Japan's version of NXT", but that was never the case.
The whole thing didn't work at all. Fans got legit pissed at some of the angles they ran and even though they were helping with salaries, New Japan couldn't find a better TV deal nor sponsors to help NOAH out, so their business was as horrible as always. So Marufuji, who was pretty much running NOAH in 2016, pulled some strings and got another company, Estbee, to buy NOAH out. Thing was, this was made without New Japan's consent, so the relationship broke in bad terms.
To be honest, New Japan never really cared about making NOAH profitable and it always seemed they were doing charity and wasting Suzuki-Gun (or shoving them down NOAH's fans throat, depending on your POV) for no good reason. Maru did the right thing for his company, but kicking one of your main partners out, behind their back will always cause bad blood I guess
.