Is there a way to make mods using Unity Free

I intend to release the hole project with the unity project or (as much needed) attached so that the player can mod the it easily. What is the best approach so the player can make their own missions?

UA is generally not the place for any questions that ask for the “best approach”, since that almoist always implies subjectivity in the responses.

You can distribute your entire source of your project if you want and let people modify and compile it themselves. Or you could build a level editor in the game itself. Or you could make all your missions be defined by structured external files (e.g. XML, TXT) that are loaded in at runtime, so users can define their own levels by just adding new files to the directory. But which is *best"? No idea.