Raiden managed to take down Mistral, one of Desperado's top cyborgs, but the PMC group continues to run rampant. Now they've set up a research lab in Mexico, and Raiden - with some extra help - must infiltrate the place and figure out what they're up to.
After escort Wolf runs off (yep, he's on your side now), Raiden will be left to his own devices. Follow the pooch down the tunnels. Check straight ahead at the first split for some Repair Nanopaste and to the left to proceed. You'll almost immediately be confronted by a hulking UG called a Mastiff that wants nothing more than to squash Raiden.
This fight is surprisingly hard, considering this thing is just a normal enemy. Parrying is always your best bet, though it can be difficult to get these things in front of you when they attack. Keep running and dodging until the Mastiff is in front of you, then prepare for a drop kick which you can parry. Wade in and attack a few times before retreating. Be careful whenever the Mastiff glows golden, as it will try to grab Raiden. Leap out of the way and avoid its attack and it will fall, giving you a brief opportunity to slice it up. Use Blade Mode even before going for a Zandatsu kill is recommended, as taking out its arms will reduce its attack options.
Go up the stairs in the tunnel beyond. You'll come out above two Mastiffs patrolling the sewers. One was tough enough; don't try to take on two just yet. Get the one below you easily with a Ninja Kill, then run (but don't Ninja Run) down to the other end. You should have just enough time to Ninja Kill the second Mastiff before it can turn around and notice you. You also have the option of bypassing both by checking the wall to the right in this tunnel, where you'll find a small side hallway containing VR Mission 005.
Slice through the fencing to the left in this tunnel and drop down into a lower sewer. The ceiling of this tunnel is lined with Dwarf Gekkos just waiting to drop on you. Use the EM Grenade sitting off to the left of the tunnel to bring a lot of them down stunned and slash them apart. Not difficult, just annoying. Keep killing them, and check the boxes along here for a Hold Chip and an Electrolyte Pack. There's another EM Grenade at the end of the tunnel.
Slice through the bars to your left. After a short jaunt you'll wind up in a cut scene, and Raiden will be facing down three new robotic creatures. They're called Raptors, and surprisingly enough these three together are probably easier than a single Mastiff. EM Grenades are incredibly effective against these guys; throw one and you can stun all three temporarily, giving you plenty of chances to get in strong shots. Keep Ninja Running to avoid their gunfire, and parry whenever you get a chance to push them into proper stun. Then slice them open with Zandatsu. The only thing to really watch out for is the purple light they emit, which will stun Raiden temporarily and give them plenty of chances to stomp him down. Get away from the Raptors whenever you see even a hint of purple light.
In the aftermath Raiden will meet a rambling boy named George, who has more than an inkling regarding the whereabouts of the research lab. After he's done chatting away, backtrack to where you fell down to find a Grenade in a box before proceeding to your next destination: a door. Slice through it and the next door to find a small room. Inside is VR Mission 006… and… oh lord. A Cardboard Box. You'll have to use this stupid thing to get through the next area, which is crawling with Mastiffs.
There are two ways to do this. The first is to equip the Box as a Sub Item and use it to slip through here undetected. It's pretty easy to get at least one of the Mastiffs off-guard using the Box, so long as you don't move when they're looking your direction. (Make sure to hold down the trigger to keep the Box on your head.) More than likely you'll have to still fight one, though with some caution you can Ninja Kill all three. If you're lucky you can slip into the room on the bottom floor and get away before any of them see you, finding a Hold Chip for your troubles. The second (and generally unadvisable) way through here is to challenge all three to a fight. One is annoying; two is hard; three is near-suicidal, unless you're really, really good. Don't try to fight all three. Regardless of the number you fight, stay mobile and check the boxes on the bottom of the sewer for power-ups.
Once the three Mastiffs are neutralized, you'll receive notification of backup in the previous sewer tunnel, where you fought the Raptors. Go back and you'll find a new mech waiting for you: the Vodomjerka. This water-skimmers will either rush you, burn you, or spin out and slam you around. The easiest way to kill one is to run to the opposite end of the tunnel while it's using fire. This will prompt it to rush you - an attack you can easily parry. Do this and damage it to stun it, then take it out with Zandatsu. You'll face one solo, then one with Dwarf Gekko, then two at once. None of these fights are terribly difficult. You can also check the walkways and pipes above for a Data Storage.
Either way, you'll wind up in another tunnel system that runs roughly in a square. There are Vodomjerka in here you can fight - they'll keep respawning when you kill one, though only up to five or six - but you can avoid these mechs by travelling the circuit of the tunnels behind them. Slice through the wall at the waypoint and you'll find your way into the research facility.