Kickstart with Azure AD Applications and Microsoft Graph API: concepts, architecture, mechanisms, toolbelt
Microsoft Graph API, previously known as Office 365 Unified API, is a new way how to access and manage productivity data and logic. It is now a preferred way to develop for Office 365, and more than Office 365. "One endpoint to rule them all" is the official Microsoft's slogan for Microsoft Graph.
Preferred way to deploy the applications which use Microsoft Graph are Azure AD Applications. Azure AD is much more than managing users: it can, and it should be used to manage users, applications and devices. Through this triangle, admins can fine-grain who can access which application and data, on which devices.