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While Prototype focuses heavily on intense close quarters combat with multiple foes, Alex will also need to infiltrate military bases to complete events and missions or to gain access to information about how to better use vehicles and weapons. Completing these missions can be tough, but in some cases it is the only option. Even a being as powerful as Alex can't go toe-to-toe with the military in every situation.
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The Basics of Stealth
The entire stealth system in Prototype revolves around the little bar on the right side of the mini-map which constantly shows Alex's position. This bar tells the player how close Alex is to being revealed. When Alex is being detected by viral detectors or other enemies with means to unveil him, the bar will begin to raise and become orange. When Alex is detected it becomes red.
The situations which will cause the bar to raise or to possibly become red instantly are very specific. Using Alex's non-combat powers, for example, will not unveil him or making him more likely to be detected. In fact, it is entirely possible to spring from a skyscraper rooftop and land directly in a military base without anyone in the base being concerned - so long as Alex is in military disguise when he does so.
Alex always has two forms available to him. One is his disguise form, which will be whatever human enemy he last consumed, and the other is his normal form of Alex Mercer. These two different forms are separate in terms of being considered detected. Alex's normal appearance will also raise an alert if a military member sees him. That alert does not extend to his disguise, however, as long as Alex does not switch forms in plain sight. In addition, any disguise Alex has assumed will begin to lose its alert level if Alex switches to and spend time in in his normal form. This is the primary way of getting out of tough spots - switch to Alex's form, wait for the disguise to lose its alert, then find a hiding spot and switch. Presto! The military will lose track of Alex.
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Breaking into a military base is one of the most challenging stealth tasks that Alex will face in the entire game. Military bases are filled with personal, making it difficult to use stealth consume, and there are usually three viral detectors.
When breaking into a base, getting rid of the viral detectors is a first priority. Approach in military disguise from the fringes of the base. The viral detectors do stack when it comes to raising the alert level, so getting caught in radius of all three detectors at the same time (which means Alex would be in the middle of the base) is bad news. Play the mini-games to deactivate each detector - this should not take long.
With the detectors disabled, find the base commander whose form Alex needs to take to gain entry into the base's interior. A stealth consume may or may not be possible. In some cases, there are simply too many soldiers around. If that happens, Patsy is Alex's best friend. Find a soldier and use Patsy. The enemies will target him, the alert level will be lost, and Alex will be free to enter the base.
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On the Road
Besides the viral detectors in the bases, Alex also has to deal with viral detecting UAVs in the field. These detectors can be problem for Alex if he's not paying attention. Always keep an eye on the mini-map and watch out for the little white circles which indicate the area of effect for the mobile viral detectors. These detectors do have a vertical reach, so if you're on a building above them they will still raise your alert level.
Eliminating these detectors can be a problem because there is no sabotage mini-game as in the case of the viral detectors in bases. That means that to get rid of them, Alex will have to attack them. And attacking them means unveiling himself.
Most of the risk of attacking the detectors can be negated, however, by using Alex's throwing abilities. Given a long stretch of street or a roof-top, Alex an hurl cars or AC units at the viral detectors from several blocks away. This will still unveil Alex, but if there are no soldiers in the immediate area to see him a strike team probably won't be called in. Using this method, Alex can get rid of mobile detectors without seriously compromising his position.
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Good 'ol Patsy
Dealing with the viral detectors are the only stealth situations which provide a major challenge to Alex. The soldiers are shockingly dumb and will not raise an eyebrow if a disguised Alex runs past them, flipping over cars and throwing bystanders through plate-glass windows. If Alex is ever in a situation that seems difficult to get out of, remember Patsy. Patsy is Alex's get out of jail free card. It almost always works at getting rid of Alex's threat level and ensuring that Alex has a second chance.