The film begins in a close up on Alma, whom Reynolds has yet to meet, discussing her relationship with the fashion designer. We know that she gives all of herself to him. Reynolds is a difficult man; he desires imagination and creativity and discipline in a way that would exhaust most within hours. Nonetheless, he's skilled in a way that has brought prosperity to his family, brought a name and a status in society which is very much about social standing. He does not want to let that go, and every moment that distracts him from continuing to have this he repels, including Johanna who he sends away for having a conflict with him at the breakfast table the morning of a fitting.
Enter Alma, who falls, or trips rather into Reynolds' life. She becomes his muse; he's inspired to create from her body. But, his routine does not change and this frustrates Alma who is as strong-minded as Reynolds is, but what she desires is a deeper connection with him, not only work. She wants to be let into his life, not just his work.
Alma has seen Reynolds from the very beginning. She knows he is strong, but that he is strong in order to hide the weakness within him. She has been able to truly see him in a way that is terrifying for him as it throws his world into chaos. So much so that he desires to get rid of Alma, but is, possibly for the first time torn as he also desires to keep her in his life.
She is the phantom thread. How does he keep her, and create with her? He does not know, but she demands he learn to trust her in a way he's never trusted anyone before. The only way she sees to do this is poisoning him in order to weaken him so that he can be vulnerable and let his pain and weakness out so that he can be truly strong when his health returns. This becomes their secret, a game they play that is quite mad, but to them allows for them to make sense of the chaos. Thus, they create madness in their life in order to maintain the element of genius - for better or worse.