By early 1985, the Macintosh's failure to defeat the IBM PC became clear,and it strengthened Sculley's position in the company. In May 1985, Sculley—encouraged by Arthur Rock—decided to reorganize Apple, and proposed a plan to the board that would remove Jobs from the Macintosh group and put him in charge of "New Product Development". This move would effectively render Jobs powerless within Apple.In response, Jobs then developed a plan to get rid of Sculley and take over Apple. However, Jobs was confronted after the plan was leaked, and he said that he would leave Apple. The Board declined his resignation and asked him to reconsider. Sculley also told Jobs that he had all of the votes needed to go ahead with the reorganization. A few months later, on September 17, 1985, Jobs submitted a letter of resignation to the Apple Board. Five additional senior Apple employees also resigned and joined Jobs in his new venture, NeXT.

The Macintosh's struggle continued after Jobs left Apple. Though marketed and received in fanfare, the expensive Macintosh was hard to sell. In 1985, Bill Gates's then-developing company, Microsoft, threatened to stop developing Mac applications unless it was granted "a license for the Mac operating system software. Microsoft was developing its graphical user interface ... for DOS, which it was calling Windows and didn't want Apple to sue over the similarities between the Windows GUI and the Mac interface." Sculley granted Microsoft the license which later led to problems for Apple. In addition, cheap IBM PC clones that ran Microsoft software and had a graphical user interface began to appear. Although the Macintosh preceded the clones, it was far more expensive, so "through the late 1980s, the Windows user interface was getting better and better and was thus taking increasingly more share from Apple". Windows-based IBM-PC clones also led to the development of additional GUIs such as IBM's TopView or Digital Research's GEM, and thus "the graphical user interface was beginning to be taken for granted, undermining the most apparent advantage of the Mac...it seemed clear as the 1980s wound down that Apple couldn't go it alone indefinitely against the whole IBM-clone market".