If you host, the story will progress at your pace. If your friend is hosting you can play any mission with them but you won't unlock those missions for single player before you've completed the prior missions. Your level and loot is saved as the multiplayer is drop-in / drop-out.
Also feel free to join us in Discord
There's plenty of active Alienation players if you ever need someone to play with.https://discordapp.com/invite/ZdgcQrb