Question: What is the best file format for multiple systems?

I am developing an application which is similar to an encyclopaedia. There will be over 2800 sections and it will work on web and mobile devices (native – I need native for system tools etc and voice search). I wanted to know if anyone has any recommendations for which file type to use. Each file is a separate section of the app and will contain Text (Headings and lists etc), Tables, Images, Flow charts and links to other sections. Someone has recommended Markdown and I have been using HTML for testing. Does anyone have any recommendations and what do other people use?