Investigative journalism is based on understanding how systems work or supposed to work – that is likely how you have found your story and planned investigations thus far. To get answers, frame your questions in the following manner: How is this process or system supposed to work? Who is supposed to do what, when and how? How is the process documented and recorded? What standards or benchmarks will be in place, how are they established and who enforces them? The more detailed and comprehensive the answers will be, the better you will be able to judge where and when things may go wrong.
Additionally, it is important to keep track of the chronology in your investigation. This does not mean that you have to present your story in a chronological way, but rather that you 'pin' found facts on a timeline of the events. This will help you to build a clear picture of what came before and after, and what happened simultaneously.
You will also need to differentiate between qualitative and quantitative knowledge. Quantitative is about placing numbers on the map. For instance, how many quality checks does a certain medicine need to undergo? What is the level of pollution in a water body? How has city crime trended over the past five years? Very often, it is the figures that can turn a small local story into a major national investigation by providing concrete evidence, like school dropout figures in your community that may also resonate with the entire country.
In contrast, qualitative mapping is about people, events, reasons, motivations, feelings and arguments. In many places around the world, it is hardly possible to access quantitative or written records simply because there are not any. But there are two other ways to investigate issues in such a document-poor environment: through use of your own observations and structured interviews of relevant people. This is how you can build your own database. Keep in mind that starting with an issue often leads you to a person or group of people, but profiling databases works also the other way around: a piece of land or a street address can lead you to the owner.
To organise all the researched information, there are electronic project management tools that allow you to create a database of interviewees, knowledgeable contacts, informants and their areas of expertise. It should contain a catalogue of questions, fact-sheets to help you record established facts as well as assumptions that still need to be proved, plus hyperlinks to relevant documents, facts, statistics, databanks, minutes and interviews. Evernote is very popular among journalists but not secure enough to store classified information. Keep in mind security when choosing a management tool.