The Missile Silo
We get dropped off by the front gate to the missile complex, but it is locked. No matter, simply follow the fence and play with the doggies - there are two on the northern side, two on the southern side and one to the west - until you've reached a two-floor hut, connected to the complex with a walkway. Make sure you stay close to the wooden fence, by the way - there is a sniper on that tower overlooking the complex. Approach the hut to hear three MJ12 troopers discussing recent events at the site, then either try to lure them outside or simply rush them inside; when in doubt, keep an eye on the guy with the sniper rifle first. With the unwelcome company gone, collect the goodies - there are two 100-credit chits, four cans of soda, a bag of soy food (in the smashable trunk) and a key to the front gate on the ground floor, a multitool on the first floor and a lockpick, a biocell and a medkit in the attic (accessed using the keypad on the first floor, once again accepting a certain two-digit number).
While we are now right next to the walkway leading into the complex, we won't be taking it - not with the sniper on the tower and two security bots wandering around in the area. Instead, head back to the front gate and use the key to open it, which will place you in a very good position to climb the tower and eliminate the first part of the problem. Now, look down at the building under the tower. Jump down onto its roof after the sentry patrolling it has gone back inside, but don't wait for him to come back to investigate the noise - instead, head west along the northern edge of the roof until you've reached another walkway, cross it and enter the hut on the other side. You can relax for a while if you need to, the hut cannot be accessed from the ground level. Take the ladder down, you will find a repair bot, a multitool on one of the machines and a lockpick on the table. Moreover, there is a vent there which leads straight into the missile complex... Enter it and head downstairs.
All the blast doors but one can be opened using the code Savage has broadcast to us at the beginning of the mission. Don't worry about the exception, we'll get there soon enough - meanwhile on the other hand go into the tunnel to the east with laser beams at its end. There is a panel at the beginning of the tunnel which can be used to disable those beams, do so - in this case it will be much better not to trigger the alarm. Carefully make your way towards the end of the tunnel, keeping an eye on the commando patrolling there; veer left as you come close to the end to stay out of sight, then bop the fellow (as quietly as possible, in preference) when he turns his back on JC. Afterwards hear up the nearby stairs and make short, silent work of the two MiB sitting at the launch control consoles and their companion watching computer banks nearby. You can now abort the launch as instructed by Savage. If you can hack you can enter the new target as well, otherwise you'll have to head downstairs into the locked bathroom, which you can either unlock or enter from above, staying wary of the spider bot roaming there (and guarding a lockpick), and read the DataCube lying there. Either way, make sure you talk to the scientist imprisoned in the bathroom after the co-ordinates has been changed - he will tell you about an ambush on the way to the missile silo and how to avoid it.
Leave launch control and go through the previously-closed blast door. Once you've reached the tunnel with metal grating on the floor and Page starts talking, you will know this is the place the scientist has been talking about - so look down, move one piece of the grating aside and jump into the duct there before you are given the announced warm welcome. The duct will lead you to the pool of water at the bottom of the silo.
Dive and press the button close to the floor to call the elevator. Once it's arrived, there are several levels - from 2 to 6 inclusive - to choose from as our destination. I will briefly go through each of them:
- this is where Howard Strong is trying to sabotage the missile. Head right quickly after you have arrived, if you do it right the guy won't notice you - giving you ample time to walk to the platform lift he is on, climb onto its motor, walk up the lifting arm (speed augmentation helps here, but isn't necessary) and deliver some concrete arguments to his thick skull.
- just a few spider bots, avoid.
- a repair bot! Definitely a good place to stop by, just make sure you aren't seen by the fellows above.
- here is where the ambush party - a MiB and two commandos - was waiting for you. The meticulous ones may want to stop by and put them all to sleep, otherwise nothing to see here.
- the topmost level, with one Man in Black guarding the ladder leading to the surface. Handle him as you see fit, then leave.
This is basically it as far as the mission objectives are concerned, so you may simply talk to Jock and proceed to admire the effect of your handiwork at the Area 51. Then again, we haven't had too good a look at surface of the missile complex - and while neither the stairs nor the elevator to the silo will be of interest to us, there is also that building we jumped onto from the tower and a trailer parked nearby. The building houses four troopers: one patrolling the big room to the east on the ground floor, one sitting in that room, one sitting at a desk upstairs on the western side and one walking into this room and out to the roof. Both ground-floor doors leading inside can be power-smashed, but better do that on the western one - there are smaller chances of being heard by the troopers and you can still get to the other section via an air vent. Regardless of whichever order you took the four guys in, get the trailer key from the big room - then walk to the trailer and get the medkit. Yes, that's the only useful thing there!
Get on the helicopter and watch the missile fly.