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You've been assigned to the task of stopping a nuclear missile. No problem. When you land, you'll be next to a large square enclosed area with several small buildings. Inside the fence is also a guard tower - with guards - so if you don't want to be spotted, hug the fence. Nearby where you land will be a locked gate. Depending on whether you feel like expending the lockpicks, and if you want some decent supplies, we can find the key.
Hugging the fence, head around the corner to the left side, where two doberman's are patrolling. They're easy enough to take out with a single tranq each. Continue up the left side to a small building with three guards sitting at a table. As they talk you can listen in, and when you're ready, open the door and chuck a gas grenade inside. Take them out as you please and then grab the front gate nanokey off the table. Head upstairs.
The keypad up here requires two numbers, so here they are: "12". Input those numbers and watch as another staircase descends. Climb it to a small upper attic with several crates full of worthwhile supplies.
On the second floor of the building you'll see a door leading to a catwalk which takes you into the compound. Let's use the front gate. When you backtrack to the front and open the gate with aforementioned nanokey, you'll notice a couple of the smaller (but not smallest) bots patrolling the area, mainly on the right side.
If you wanted to explore, it's a bit tough in this area without killing or alerting anyone. In the first building to your left are three guards, and attached to the one behind it, a catwalk to the building on its own right, which houses is a repairbot and alternate entrance into the missile silo. The easiest way I've seen, however, since the items are not very good here, is to break directly in. Therefore, head to the far right where you'll see an aluminum fence surrounding a square area with a door. Keeping aware of the robots nearby, enter the area and hide behind the small building until one passes, then throw a LAM in front of the door to blow it up (STR of 25%). Or, simply lockpick it. Descend all the flights until you come to a keypad connected to a large door.
You were given the silo code at the beginning, 8456, so enter that into the keypad, slip into the next room, again enter the code on the keypad, enter the next room, and yet again, enter the code on the keypad on the left door. The right door in this room is the missile silo door, and will be closed until you complete your initial mission. Enter through this last left door and you'll come to a long hallway with laser grid at the end, and electronic panel nearby you.
A choice. Behind the laser grid there is one MJ12 commando and three MIB upstairs. If you wait for the commando to walk by the laser grid and snipe him, the three MIB will come. They're not that hard with a sniper rifle or other good gun. Then you can simply walk through the laser and ignore the alarm. Choice #2. Disable the laser, walk quietly up to the laser grid area, wait for the commando to pass and quickly walk up behind him and use the prod on his lower back, for the pure stealth solution. Upstairs will still be three MIB with their backs turned that you can do with as you please, even downing two with prods before they notice and the third even if he notices. Or, use Cloak and nevermind the above :).
However you choose to proceed, get past the laser, take a left once inside the far room and another left at the corner. Unlock the door using lockpicks to reveal a captive scientist and datacube on the sink which tells you the logon: "elder" and "armageddon". In the back of this area is a crate with 30.06 ammo. Head upstairs where, if left undisturbed, three MIB will be, two sitting. You can prod these two and take the third standing near the tape backup drives (?) however you wish. When its over, open the abort cover where one of the MIB was sitting at the desk, and hit the switch. Now notice the security panel to your left revealed behind the red glass. Use the logon "elder" and "armageddon" to initiate the new launch, and then backtrack to the once-locked and closed missile silo door; it's now open.
Enter the room, and at the foot of the hallway there's a grate. Open it, drop down into the shaft (noticing the ambush way down the hallway), and follow it until you drop into a large round pool of water. Your goal is to knock out or take out Howard Strong on level 2. An easy way to do this is to swim to the north side of the tank and look up. You'll see a small crane with a man in the booth at the top. That's Howard, so use your tranq gun or any other of your choice and take him out. As you receive an incoming message, swim below surface and press the button on the elevator lift. When it comes down, you'll have floors 1 through 6 to choose from. Floor 2 is Howard Strong, who has some supplies on his body if you climb the crane. Floor 3 has two spiders. Floor 4 has a repair bot. Floor 5 has an MJ12 commando and MIB. Floor 6 is actually where we want to go eventually, where an MIB awaits. Cloak or take him out as you please, and climb the ladder on the 6th floor to the hatch. Press the switch and climb out to see Jock's chopper awaiting.
Though there's some talk of celebration, you say your mission is now to take out Page himself, who is at Area 51.