Prototype Guide - Walkthrough
A New Order
Before starting this next mission, you'll want to visit the two Military Bases currently on the map and Stealth Consume the marked officers there to acquire the upgrades they offer. From now on, bases that contain a Web of Intrigue target or one or more officers that yield an upgrade when consumed will have a plus sign affixed to the Military Base icon on the city map. There is one such Military Base at this time.
Infiltrating a Military Base is simple. First, you must assume a military disguise to enter the perimeter of the base undetected. If you don't currently have access to a military disguise, try to Stealth Consume one of the soldiers patrolling the streets outside the base. Once you have a suitable disguise, you'll need to locate the base Commander. The Commander is distinguished by his short-sleeved shirt, fitted military cap, and sunglasses. When you've found the Commander, use Stealth Consume to assume his identity. Then, stand in the yellow marker outside of the base and press the Y/Triangle button to enter. You're in!
Assume the identity of the base Commander to gain entry to the Military Base undetected.
Once inside, you should notice one or more marked units. Units marked by a blue DNA strain icon yield an upgrade and perhaps a Web of Intrigue node when consumed, while units marked by a red profile icon are Web of Intrigue targets exclusively. You'll want to Stealth Consume these targets before alerting the military to your presence. Follow the target around until they are out of sight of the other soldiers and perform Stealth Consume to acquire the upgrade or Web of Intrigue node. If it helps, try stealth consuming nearby soldiers to ensure that you are not being watched.
You'll receive a Stealth Infiltration and Base Capture EP bonus after consuming each of the marked targets in the base interior. If the military is alerted, the base will be locked down, and you'll be forced to fight the waves of soldiers that come through before you can set back outside. Alternatively, you can easily evade the military to end the alert by ducking behind the munitions crates on the raised platform as Alex Mercer, waiting until your military disguise is safe to use, and then switching back to it.
Consider destroying the Military Base once you have acquired the skills from each marked target, as doing so yields a large amount of EP and will cut down the military presence in the area of the city the base is situated.
To level the building, you need to damage its exterior considerably. Outside, you'll need to get your hands on a Missile Launcher, or find a tank that can be used to significantly damage the building. Cause a stir to alert the military, and then hijack one of the tanks that arrive. Once in a tank, start by blasting any other manned tank in the perimeter, and then turn your attention to the building. Hit the building with primary and secondary fire until it crumbles.
Before starting this mission, be sure to purchase the Hammerfist Power upgrade. When you're ready to begin, stand in the yellow marker outside of Karen Parker's Lab and press the Y/Triangle button.
Mission Objective: Collect Genetic Material from Infected Water Towers
Follow the marker on the mini-map to reach the Infected zone. Hit the marker on top of the building that you come to, and then read the pop-up that appears onscreen. You're tasked with collecting Genetic Material, and you'll initially be targeting Infected Water Towers. Infected Water Towers house Hunters, and will erupt if you remain near for too long. Destroy the Infected tower before it erupts, however, and the Hunter inside will die and release the Genetic Material you seek.
The Hammerfist Power is best used to bust an Infected Water Tower before it can hatch. If you haven't acquired this upgrade yet, do so now if you have the EP to spare. Select the Hammerfist Power by holding LB/L1 and selecting it from the upper half of the power wheel. With Hammerfist equipped, Glide to the marked water tower and land on top of it or at its base. Quickly tap the X/Square button twice to perform a couple of attacks, effectively destroying the tower. Collect the yellow orbs to partly fill the Genetic Material meter in the top-right corner of the screen. Fill the meter completely in this fashion to complete the objective.
Use the Hammerfist Power to destroy the Infected Water Tower before it can hatch.
If you are not quick enough and the Infected Water Tower is able to hatch, one or more Hunters will be set loose. Ignore them, and instead follow the red skull marker on the mini-map to reach the next Infected Water Tower.
Mission Objective: Collect Genetic Material from Hive
Once you've collected enough Genetic Material from the Infected Water Towers, you'll need to collect more from the Hive in the marked Infected zone. The Hive consistently manufactures Genetic Material, but the military is currently working to destroy it. You'll have to defend the Hive from the military until you manage to collect an adequate amount of Genetic Material.
If you have EP to spare, acquire the Hammerfist Smackdown upgrade via the Upgrades screen. This attack is particularly effective when used against tanks, which is what you'll be up against while in the Infected zone. Hit the marker atop the building across the street from the Hive to get started.
The Hive at the heart of the Infected zone will regularly spew out Genetic Material, which appear as yellow orbs in the world. To finish this mission, you must completely fill the Hive Genetic Material meter in the top-right corner of the screen by collecting the Genetic Material output by the Hive. A message will pop-up onscreen each time the Hive loses a quarter of its integrity; if the Hive is destroyed and you have not collected enough material, you'll fail the mission and have to retry.
Hunters—and soon the military—occupy the Infected zone. The Hunters are a nuisance, but can be ignored, and may even help you fight off the military.
Collect the Genetic Material that the Hive spews out before it's destroyed.
Start by sprinting around and collecting the Genetic Material peppered throughout the area. When the military arrives, destroy each of the tanks that roll in using Hammerfist Smackdown. The Tanks may be destroyed by the Hunters as well, but make certain that there are no tanks in the zone, as they can inflict a large amount of damage on the Hive. Alternatively, you can hijack a tank and use it to destroy the other tanks, as well as the Hunters. Note that you cannot pick up Genetic Material while in a tank, so you would have to occasionally hop out to do so.
The second largest threat to the Hive are soldiers equipped with a Missile Launcher. Once the tanks have been dealt with, continue to Sprint around the area collecting Genetic Material, but whenever you spot one of these troops, prioritize killing them. If the military calls in the Strike Team, ignore the helicopters that arrive, as they don't seem to be interested in attacking the Hive.
Continue sprinting around the zone collecting Genetic Material, destroying any tanks that appear and killing any Missile Launcher-equipped soldiers that you spot, until the meter in the top-right corner of the screen is completely full. Mission complete!
Once you've completed the mission, consider hijacking one of the tanks in the zone and using it destroy the Hive, as doing so yields a significant amount of EP and will cut down the amount of Infected in this area of the city for a short period.