Are you supposed to disclose all stimuli that your participants have been exposed to? I am a master student in psychology in the US.
I performed a study in which the participants had to read a story and should recall it afterwards.

Now I am writing a manuscript where I only analyze parts of the participants’ responses to answer my research questions.
This puts me in a dilemma: Should I explain the whole story stimulus in my paper or just focus on the parts that I analyzed?

My supervisor suggested that I should not mention the unanalyzed parts of the story at all because that will distract readers and take away the focus of the paper. However, I'm thinking what if this paper is published and someone ask for the stimuli to replicate the study, and then find out that the stimuli is different from the way I presented in the paper. It’s like I’m hiding something from them. I worry this may lead to a retraction of the my publication. I’m very new to academia and my supervisor sometimes is not very on top of things, I don't think he cares much about what I do. So I want to make sure I do the right thing and ask for your advice.
Psychology is not my field, but your concerns seem valid to me. As a reader of your work I'd want a fairly complete picture of the experiment that was done. 

However, you don't need to discuss everything at the same level of detail. A synopsis of the parts you don't focus on is likely enough to satisfy your concerns without distracting readers from what may be more important to your purpose. 

In other words, the overall description can be broad, but not deep. Then focus on what you want to say. Arguably, the fuller description could come in an appendix/annex to the paper. Or if a fuller description of the experiment has been published you could just cite that. 

If I think that the "unexplained" parts are more important to the outcome then I, at least, have a basis for discussion, rather than having just been misled. 

But, again, this is advice from an outsider.