This is the plan or set of steps to be followed in a study. In a clinical trial the protocol should set out the study design, the entry criteria for patients, and any exclusion criteria, the treatments, dose, duration, outcomes (both the efficacy and adverse events, and how they are to be measured), and analysis plan, as a minimum.
A protocol for a systematic review should describe the rationale for the review; the objectives; and the methods that will be used to locate, select and critically appraise studies, and to collect and analyse data from the included studies.
Protocols can, and probably should, be amended. A plan may change because the nature of a trial or review changes. The key thing is that the amendments to the protocol need to be noted, together with the reasons. Protocols are good things because they make you think about what you are going to do, and why.