When you leave to the main menu and select your save file, there should be message window asking if you want to continue from the level you reached. Like here, for example: https://youtu.be/pMzSpaDM6kU
If you choose to not continue previous run, you loose all silver and artifacts that you found and will need to collect them again.
To bring everything to base you either need to get to one of two retreat points (red car) or to complete the mission.