This location is divided to two parts; the main building which can be accessed anytime and the underground Command Center which can only be accessed during the main quest "Reunions". The main building's entrance is blocked so you have to enter from the south, through the 2nd basement level of the parking garage.
Main Building
From the stairs, the green steamer trunk is found to the west but the door is chained on the other side. You have to make your way around to reach it. The room in the NE corner has an Advanced Floor Safe and a bobby pin box. The laboratory on the SE has a chem station and an explosives crate. Make your way to the NW to reach the room where the steamer trunk is located.
The Advanced terminal there can be used to open the locked security gate in the same room, containing various loot.
In the upper floor, the room to the NE has a cooking station, and Advanced Wall Safe. In the kitchen to the SE, there’s an issue of Guns & Bullets on the table.
Command Center
This lower part of Fort Hagen is only accessible during the main story quest “Reunions” where you need to confront Kellogg. From the room with the green steamer trunk, take the elevator going down. Take note that this elevator will only become active once you start this quest.
Follow the straightforward path until you reach a security door. It has a pressure trap that will trigger when you open the door. Make sure to disarm it first before opening the door.
Follow the straight path until you reach a sleeping quarters with lootable footlockers. In the next room, there’s a Novice security door with some loot inside.
In the generator room after the corridor with laser turrets on the ceiling, you can find a Fusion Core.
Continue past that and in the corner, the blue double-door is a clinic where you can sleep and gather Aluminum surgical trays. In the dining room across that clinic, you can find an Energy Weapons Bobblehead on the metal table between two fridges in the kitchen.
Outside the kitchen, you’ll see two doorways. Enter the maintenance tunnel to the right first and you’ll find a Nuka-Cola Quantum beside the skeleton and a toolbox containing the Fort Hagen Armory Password.
Continue to the other tunnel and you’ll find the armory in the end of the tunnel. Open the security door with the Fort Hagen Armory Password to access all the goodies inside, including a mini-nuke and a Fat-Man.
Next to the armory is a bedroom. There’s an issue of the U.S. Cover Operations Manual there.
The next rooms has a few more loots. Beyond the red double door is where you'll find Kellogg during the quest. In the control room where you fought Kellogg, you’ll find another green steamer trunk, and an issue of Robco Fun under the table near his terminal. Once done, you can leave the area through the elevator to the south.