With the expansion of The Minutemen's settlements, The Institute now sees the faction as a viable threat. After completing Form Ranks, this new quest will automatically start. The first two steps are to reconvene at Fort Independence and speak to Ronnie.
You'll have a brief window of time to build defenses in and around the fort. Ideally, you should have enough materials to meet the 100 percent fortified goal. Reaching 100 percent is unnecessary, but it obviously helps to have as many turrets as possible for backup.
As a fort with multiple entry points, be ready for Synths and Coursers coming in from all sides. Assuming you're well stocked on ammo, you should be able to withstand the multiple waves of Institute soldiers. The Minutemen are often helpful, so even if you have to hide for a moment to heal or manage your inventory, your buddies will cover for you.
Once you've repelled The Institute, speak to Ronnie, and then speak to Preston to complete the quest.