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You've talked with the leader of the NSF terrorists at the top of the Statue and have headed back to UNATCO HQ to speak with Paul at the entrance, who will tell you Mr. Manderley wants to speak with you inside.
There are a couple of things you can do here, but why not get the outside area done first. Go through the main doors and speak with the UNATCO receptionist (male) sitting at his chair in the lobby. On the desk is a datacube with a code: 0451. Head back outside to the small building to the west, and use the code on the access panel to the door. Inside, you'll find some ammo and a computer panel that can open the outside trap door, which contains another exploration bonus and more supplies. Head back inside when you're through.
Continue on inside through a long corridor that requires loading a new area, and use the retinal scanner further inside to gain access to the office levels 1, 2 and 3. On level one, you'll notice a pair of locked office doors which you'll come back to later. Down the stairs, the right side of level 2 has your personal office, in which you gain a small bonus and can login to the computer and check your e-mail with the access codes Alex coms to you once you enter. You'll want to meet and talk with Anna, your new partner in the break room past a couple of doors next to your office. That will complete a secondary objective
Manderley's office is next to the break room on level 2, but you'll first see the receptionist. Grab the nanokey off her desk, and the datacube has his computer logon codes.
Speak with Manderley for an update and bonus, and to get new objectives: find Jaime Reyes for a medical exam and Sam Carter for equipment on level 3.
In the hallway near the receptionist, there are two doors that can be unlocked using the nanokey on the receptionist's desk. Each contain supplies, though one further requires a lockpick to break into.
Head down to level 3, and find Jaime and Alex J. on the right side. Anna and Sam are on the left. Might as well get healed if you're damaged now in Reyes' office. Talk with him to learn how to use the medbot and augmentation canisters, and to update your primary objective. In his office, there's a bookshelf with a plant on a shelf. Behind the plant is nanokey that opens a closet door in the area containing supplies.
Find the medbot and both heal yourself fully and install the aug canister. I'd recommend choosing Microfibral Muscle to enhance strength... allowing you to pick up heavier crates, etc., especially if you're going the stealth route.
Head across the hall to Alex J's rather large nook. On the right side of the room on the floor, there's a secret floor panel which opens that will highlight once you move your cursor over it. Step into it, turn on your flashlight and retrieve the weapon mod, office key to the level 1 locked offices, and other supplies. If you hack Alex's computer, read his e-mail to find the code to his locker within the office.
Down the small set of stairs you'll find Alex sitting at the computer. Talk to him and use the datacube if you like, which has a code you probably already have.
Exit out of his office and see Sam Carter for a stealth pistol and equipment of your choice, and to complete another primary objective.
Across the hall you'll find Anna Navarre's office, with a biocell behind her on the desk.
Now that your primary goals are complete, go back to Manderley's office and speak with both him and Paul, who's now there. He'll tell you to get to the south dock and take the boat that's docked there... leading you to Battery Park and a new mission.
On your way out, be sure to open the locked office doors on level 1 using the nanokey you got from Alex J's office on level 2, under the secret floor panel.
Proceed to the south docks and take the boat to Battery Park.