Structure

In scientific writing, chapters / sections have a typical role. Knowing what that is will help you fill these chapters in the expected way

• Introduction: motivation and management of expectations.
  
  • What is the problem?
  • why is it relevant?
  • What are you doing about it?
  • What are you not doing about it?
  Finish with an explicit (bullet-point) list of contributions.
• Background (optional): describes what is commonly known.
  The point of the optional background chapter is to present that information which is needed to understand the rest of the paper, but is already commonly known to those in the field. E.g. the sort of information you'd find in any textbook on the subject. Information that is actually new goes in later chapters.
  Background and related work could be one section/chapter. Typically, background is discussed before related work.
• Related work: (I) showing you know and understand related work, (II) newness.
  In related work you first of all show you understand work on this subject well. This not only entails describing what other researchers have done, but grouping other studies logically together and describing the various groups in a cohesive whole.
  The second point is actually the main goal of related work: showing that what you're doing is new (and aligning with previous research).
• Methodology: explaining why .
  The goal of the methodology section is to explain why you have chosen a particular approach. To that end, you compare various possible methodologies, explain their strengths and weaknesses and motivate why you choose a particular (possibly hybrid) approach.
  The full details of how your approach works are less relevant.
• Main part: your actual work.
  In the main part you explain your setup, run your experiments, design your protocol, etc. This could include any of the following, depending on your subject:
  • Design: in general, more scientifically interesting.
  • Development: in general, less scientifically interesting.
  • Setup (of experiments / tests)
  • Analysis of results
  • Validation: how did you ensure that the results are correct?
  Or, when writing a security analysis:
  • Intruder model: what are the intruder's capabilities?
  • Security requirements
  • Security analysis: why is the proposed thing secure?
    Argue this using (I) intruder model, (II) security requirements, (III) system description.
• Discussion (optional): for discussion.
  In the optional discussion section, you can discuss items that did not fit into the rest, should be mentioned, but don't warrant.
• Future work: next scientific steps.
  Future work should look ahead at what scientific questions can be done based on the work you've done. It could include some engineering aspects (refactor, incorporate XYZ subsystem, ...), but that is not its main point.
• Conclusions: scientific repeat.
  Conclusions repeat the key findings... *and* their impact. Typically, the impact is more important than the main findings. For example, "we found 37 sites out of 50 were vulnerable" is what you did. To that, you add what this means: how worrisome is this? what should be done now that we know this? How can we improve the world?