Prototype Guide - Walkthrough
Check the Military Base icons on the city map and visit any that has a plus sign affixed to it. Consume the marked units inside, and then level the place if you see fit. At this point, there are likely two such military bases; each should contain one or more marked officers that yield a skill upgrade when consumed, as well as a Web of Intrigue target.
Upgrades to consider purchasing at this point are Health Boost 2 (Health Boost 1 first if you haven't already) and Critical Mass Boost 1 in the Survivability category, as well as Consume Boost 1 in the Disguise category.
When you're ready to get started, stand in the yellow marker outside of Dana's Safe House and press the Y/Triangle button to trigger a cutscene.
Mission Objective: Investigate the Base
As you can see, there's a ridiculous amount soldiers outside of the base; as such, you'll need to use stealth to gain entry. First, you must locate the Blackwatch Commander and consume him to assume his form. You won't be able to enter the perimeter of the base without alerting the military unless you assume a military disguise. So, if you do not currently have access to an appropriate disguise, locate a soldier outside of the radius of the base on the city map and Stealth Consume him. Or, you can Sprint Grab one of the soldiers below, consume him, then evade the military and return disguised.
This base is well-stocked with Blackwatch soldiers, so don't try anything rash.
The Blackwatch Commander is marked by a blue DNA strain icon on the mini-map. Two Viral Detectors are set up beyond the walls; keep out of the white radii on the mini-map to avoid alerting the military prematurely. The amount of soldiers in the base can make it difficult to Stealth Consume the Blackwatch Commander, since you are most certainly always being watched. So, Sprint toward the Blackwatch Commander, use Sprinting Grab, then duck behind the terminal building and consume him. With any luck, you will have evaded the military in the process.
The Blackwatch Commander is 2nd Lt. Joel Brunner, a Web of Intrigue target.
Mission Objective: Stop the Military from Discovering the Safe House
Once you have assumed the identity of the Blackwatch Commander, you'll need to prevent several patrol units from discovering Dana's Safe House. Follow the red skull icon on the mini-map to reach the first patrol unit.
A mobile, unmanned version of the Viral Detector, called a UAV, is now being employed by the military. UAVs can make remaining undetected rather difficult, as they tend to follow whatever triggers their detection system. As with Viral Detectors, the detection radius of each UAV is outlined on the mini-map. In the future, avoid standing in the radius of a UAV for too long, as the longer you remain, the more the disguise meter fills. As for now, the military is on to you.
Your best bet is to hijack one of the enemy tanks and use it against them. Once you're in a tank, immediately turn your attention to any other tanks in the vicinity and destroy them. Watch out for soldiers that are equipped with a Missile Launcher as well. When the area is clear, blast the UAVs out of the sky with cannonfire. If the Strike Team is called in, be sure to shoot their helicopters out of the sky, as they can deal some serious damage to the tank.
Hijack one of the tanks and use it to obliterate the rest of the patrol unit.
When the first patrol unit has been dismantled, another will appear on the mini-map. Since there is a time limit, you have to move fast. Get out of the tank and start toward the next unit. Try your best to evade the military on your way to the next patrol unit, because while assuming a military disguise undetected, you can automatically hijack an occupied tank without having to tear open the hatch. The presence of the UAVs means you won't remain undetected for long, so quickly approach one of the tanks and hop in.
Initially, there are four patrol units, each consisting of two UAVs and two tanks. After destroying each unit, be sure to get out of the hijacked tank, as you can travel much faster while not in a vehicle. When the first four patrol units have been destroyed, three more will appear at once. This time, remain in the tank and quickly make your way to the first patrol unit. Destroy the marked units at each location to complete the mission.