Atari licensed Digital Research's GEM graphic user interface for the ST. As https://www.filfre.net/2015/04/the-68000-wars-part-2-jack-is-back/ puts it:
And of course in the wake of the Macintosh the ST simply had to ship with a mouse and an operating system to support it.
It was this latter that presented by far the biggest problem. While the fairly conservative hardware of the ST could be put together relatively quickly, writing a modern, GUI-based operating system for the new computer represented a herculean task. Apple, for instance, had spent years on the Macintosh’s operating system, and when the Mac was released it was still riddled with bugs and frustrations. This time around Tramiel wouldn’t be able to just slap an archaic-but-paid-for old PET BASIC ROM into the thing, as he had in the case of the Commodore 64. He needed a real operating system. Quickly. Where to get it?
He found his solution in a very surprising place: at Digital Research, whose CP/M was busily losing its last bits of business-computing market-share to Microsoft’s juggernaut MS-DOS. Digital had adopted an if-you-can’t-beat-em-join-em mentality in response. They were hard at work developing a complete Mac-like window manager that could run on top of MS-DOS or CP/M. It was called GEM, the “Graphical Environment Manager.” GEM was merely one of a whole range of similar shells that were appearing by 1985, struggling with varying degrees of failure to bring that Mac magic to the bland beige world of the IBM clones. Also among them was Microsoft’s original Windows 1.0 — another product that Tramiel briefly considered licensing for the ST. Digital got the nod because they were willing to license both GEM and a CP/M layer to run underneath it fairly cheap, always music to Jack Tramiel’s ears.
Just how cheap was it? How much did Atari pay DR? And what sort of terms were involved?