Second, Lysander gets lost in the forest. Third, the fairies get into the act. When Puck stumbles onto them, the complications blossom into all-out confusion before the couples are sorted out. The fairies are responsible for the confusion in the forest, the magical resolutions of the conflict, blessings of peace, and their own love story. They fight over an Indian boy, and they seem willing to punish each other if sufficiently angered.
Every plot touches the frame, and the fairy plots at some point.
The only plots that do not interact directly are the lovers in the forest and the rustics, but they come together in the final act as newlyweds and entertainers at the wedding. Shakespeare's strategy is to alternate pieces from each story, emphasizing the connections. His plays are easier to study if you comprehend each story separately, then reshuffle them to study their dependence on each other. Just because the plot is confused doesn't mean that Shakespeare was either confused or incompetent. On the contrary, he used confusion in the plot to illustrate the confusion in the minds of the characters.