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This article is a walkthrough of Prototype. It contains spoilers about the game's plot and general tactics. Please add any missing and relevant information.

Alex Mercer tries to discover who he was before he woke up in the morgue. And how a viral outbreak had occurred in Manhattan. In his search for the truth, Mercer discovers more than what he had expected.

Memory in Death[]

You start of near southwest of central park. Five Blackwatch soldier confront you. Target them and use the basic and special attacks to dispatch the soldiers. Then move further towards Times Square. You will come across a few more soldiers, this time with Missile launchers. With the Claws active, you can kill most of the soldiers with the basic attack. Consume a few soldiers or Infected civilians if low on health. Most of the soldiers with missile launchers move out of the claw's reach. Use the Groundspike special attack to kill them.

With the area cleared move further, Blackwatch has sent five Tanks to deal with you. They are marked with skull icons. Hammerfist should be activated by now. Use the Hammerfist smackdown (Basic attack) or Elbow slam (Jump and special attack), to destroy the tanks. Make sure not to make contact with any of the missiles (consume a few infected in the area).

After the tanks are destroyed, reach Times square to face a few Hunters. Most of them are distracted, as they seem more interested in destroying the military tanks than you. Wait for the military to take care of most of the hunters, while you glide and dodge the debris thrown by the hunters towards you. With the Blade power active, you can use Air slice (In Air+ Special attack) to kill the remaining. The soldiers around you are willing to help unlike the tanks. They direct their fire to the nearest hunter. With this hunter distracted, you can move in for the kill.

After the hunters are dealt with move from the area to the next checkpoint. You will see a Blackwatch officer calling a strike package to deal with the infected along with you. You have two choices here;

  • If you intend to continue a long fight, you can try to take down the Gunships and tanks. Not an easy task since they completely concentrate on you, making it hard.
  • Or you can directly sprint towards the marked target and consume him. With him consumed, the prologue ends with a tendril barrage devastator attack.

Unexpected Family[]

After the brilliant cutscene, sprint towards the compound marked and jump over the gate to escape. A transport helicopter starts to follow you, sprint through the streets avoiding the shots fired by the heli. They decide to fire at you but end up firing at a taxi. With the vehicle in your hands, target the heli and move to mark the soldiers grappling out. Aimed at the heli, throw the taxi towards it. Most of the grappling soldiers should be killed, if not you can just punch them a few times.

Run along the wall to the rooftop and you'll be promoted to climb higher. As soon as you reach higher you are confronted by two more transport helicopter. Fortunately the rooftop has a large number of air-conditioning units. Grab one, aim at a heli and hurl one towards it.

Web of Intrigue[]

You now have a Blackwatch commander in your hands, calling for help. Consume him for his memories. You learn that Mercer has a sister and the military personnel you just consumed had ordered her arrest. Disguise is now unlocked. Move towards the marker to reach Dana's house.

As soon as you arrive, you'll notice that the street is under heavy guard. Reach the nearest rooftop to scout the area, you'll notice a lot of Blackwatch soldier. Change into the commander you had consumed earlier. Drop down from the roof and walk to the mission marker.

You arrive just in time to rescue Dana from the Blackwatch soldier, who had intruded into her apartment. Dana then takes you to her friend's apartment. She points out Alex's apartment on a map.

Past and Present[]

Dana suggests you to visit the apartment Alex lived. Proceed towards the marker, You stop outside trying to recall. As you enter the apartment, a few memories of your past flashes. Before you have time to recover, you are blasted out of the building. You see a Blackwatch agent escorted to an APC. You need to consume this guy, but we have other problems now. More soldiers land near you, use the special and basic attacks at them and make sure non of them call in a strike package. Pick up one of the passing cars and throw them at the heli as well.

Note: Incase you get overwhelmed and start to lose health fast, consume the soldiers instead of killing them.
  • If the strike team is called, you have seconds before you target escapes. Evade it as you cannot survive their fire yet.
  • Alternatively you can outrun the soldiers and the strike team, change your disguise and you'll have plenty of time to reach your target.

After evading or destroying (if possible), move towards the middle of Central Park. Having a military disguise helps avoid the fight and chaos. But if you intend to be destructive, go ahead and start killing the soldiers for an RPG. Grab one and fire at the marked APC. The target should come outside of the tank, sprint towards the target and grab him. Consume your target, watch the memory and escape the scene as the soldiers aren't happy to see you. Alternatively if you still have a military disguise, transform and walk close to the APC. You should get an option to sound an "all clear". And when activated, your target walks out of his protection. Sprint, grab and consume him, then evade the military.

Behind the Glass[]

Go to Dana's safe house. She provides the location of the Gentek facility, where Blackwatch are holding another captive, known only as Elizabeth Greene. As you approach Gentek, you'll notice it's heavily guarded. Change your disguise and enter the compound, you'll notice Blackwatch has added new securities. Viral Detectors can see through your disguise, so take care not to stay long within its radius.

As you proceed you'll notice a commander, only problem here is that he isn't outside the radius of the viral detector for long. Nevertheless, approach him grab and consume. If you alert the detector and the soldiers surround you, scale the Gentek building itself, change your disguise and wait for the cool down. Glide slowly to the ground disguised as the commander you consumed.

Enter to the building and watch as Mercer walks by decomposed bodies and to the containment where Greene is kept. He approaches her but she launches herself at Mercer and visions of experiments conducted on her flash. She then turns around and leaves the building by destroying the wall. Hunters start to mass in the room and throw Mercer out. As soon as he lands, he grabs a soldier and consumes.

Sprint to the new location marked on your mini-map. Try not to stop anywhere as the hunters are following you, besides it's a short distance. Well the new location is an army base. As soon as you enter they start firing at you, but you can run around and hide behind one of the crates and change your disguise. Now go pickup the missile launcher and wait for the hunter. Take care not to get hit by the missiles fired by other soldiers. When the Hunter is stunned, and the health bar is almost diminished, approach it and consume. Mercer starts to mutate and his hands turn into Claws. With this power now unlocked and equipped, your cover is blown; the soldiers are now alerted about your presence and start firing at you. Diveroll to avoid any missiles, and wait for more hunters.

Two hunters come through the roof, concentrate at one hunter as the second one leaves to deal with the soldiers. Dodge it's attacks with Diveroll and try not to get pinned by them. Go around consuming a few soldiers if you are low on health, and when the Hunter is stunned, consume it instead of finishing it with the claws. This gives a boost to your EP and health.

Next up, three hunters. Use the same tactics you did for the previous hunter but you'll have to dodge a lot. Grab an missile launcher and launch yourself into the air. Fire the missiles, airborne as long as possible in case you start to descend, boost yourself back. After this encounter more hunters join you the rampage. This makes things a lot difficult as they can kill you pretty soon. Grab an missile launcher from the fallen soldiers and boost yourself into the air and fire at the hunters. As soon as five of them are killed, try and ignore them and let the soldiers deal with them. Wait for the mission status to change, as soon as it does use use flykick at the tanks. If there are any missile launcher you can find use them, deal with the tanks from a distance. Try to use the splash damage, fire the missile launcher in the middle of the tanks dealing damage to the one next to it. Finally the tanks explode and the base collapses, Mercer is unharmed. Power select wheel is now unlocked with many new upgrades.

The Wheels of Chance[]

You will need Stealth Consume for this mission, so hope you have bought that along with other upgrades. Fairly simple mission, you are to rescue Mercer's ex-girlfriend, Karen Parker from the infected zone. Dana informs Alex about her. Move to the marker and you'll notice that a hive has formed in that area. Ignore the Marines and infected fighting each other and proceed towards the marker. As you enter Karen is amazed and overjoyed to see you, she suggests that an APC is required to leave the quarantine zone. Head out and a Blackwatch soldier is marked for you to consume, if he's killed a second one is marked. Consume him for the location of the base to be unlocked. Ignore the soldier firing at you and the hunters, sprint away from the location.

As soon as you are out of military sights, change your disguise and proceed towards the base. You'll see the base commander strolling around, wait for him to come behind one of the trucks and use stealth consume him, keep an eye on your alert meter at all times. Now that the commander is consumed, you can proceed towards the base. Enter and you will find a few more soldiers marked. You'll have to use stealth consume if you do not wish to take on all the soldiers. Approach the marked APC driver, follow his patrol path and wait for him to reach the corner between the gas tanks to the right of his position. Consume him stealthy for high EP and leave the base without causing suspicion (Don't change your disguise and get yourself killed). You will notice an APC parked outside the base, still with the APC drivers disguise active, approach the vehicle and get into it. Drive to the west as the marker indicates and you can practice targeting here. A few Walkers approach the tank, but you can deal with them easily. After you use the main gun and the secondary weapon, return to the quarantined zone. You need to destroy the hive near Karen's apartment, remember to target the building and fire the primary and secondary weapons. Keep moving while you fire to avoid the angry hunters who will destroy the tank if you remain in one place.

With the hive now destroyed, move towards Karen's apartment. She will get into the APC, move carefully through the streets as the military has blocked the streets at a few places. Try to move around the blockade, which is possible. Do not try a rampage, if the tank is destroyed Karen dies.

A New Order[]

Karen tells you that she needs genetic material from infected water tanks so that she can test them and create an anti-virus to stop the infection. Genetic material, which are similar of golden orbs, can be collected by destroying infected water tanks before they hatch. Use Groundspike to destroy the tanks from a distance a few walkers will try and attack you, not much of a match at this point in the game. A few tanks are surrounded by the soldiers, you can either use stealth consume, kill them all in open combat or through on of the air conditioning units from a close rooftop.

Once the meter is filled, go to the Hive and you will see the military attacking the Hive. You can either battle the military and then collect the genetic material that is expelled from the Hive, or you can just avoid the military and just collect the genetic material before the Hive is destroyed. A military disguise can help a lot if you want to avoid combat with them, mind the Hunters however. If you have a military disguise, you can hijack the tanks firing at the hive and control the damage done by the military to the hive. Collect genetic material until the meter fills up completely.

Open Conspiracy[]

Dana say's that a lot of military units have been mobilized and a base has been set up near the harbor. Change into a military disguise if you have one or consume a soldier before entering the base. Be careful about those viral detector at the entrance until you can locate a commander. Run up to him and consume, doesn't matter if you are stealthy, as this commander doesn't leave the vicinity of two viral detectors. No all hell breaks loose and every soldier starts to fire at you.

Sprint up to the building opposite to the base until they lose sight of you. Now change your disguise, after his you'll have to destroy the patrols, no more stealth here. Charge towards the APC and hijack one, you can then destroy rest of the patrol at that location. Abandon the tank and move to the next location, hijack another and destroy the patrol. Follow the same routine to counter all the 5 patrols. Do not travel using the tanks as they will slow you down and you won't be able to destroy them all in time.

After you have destroyed the last patrol, you'll be informed about the remaining patrols retreating, track them down and destroy each one using the same method of hijacking a tank.

In the Web[]

In this mission, you are tasked with destroying several viral detectors spread throughout the city. A simple enough task, these detectors are fairly close to each other and are only protected by a small group of soldiers. A fairly straight forward mission, the only hindrance you may encounter is if a strike team is signaled by one of the soldiers protecting the detectors. Keep your focus on the detectors and disregard the soldiers, you can consume or kill them if you are low on health.

The Altered World[]

In this mission, you need to question McMullan about the infection, but before you can do this, you need to make sure that McMullan thinks that it is safe to land at the rendezvous area. You are tasked with sabotaging a number of viral detectors which is done by pressing the corresponding buttons that appear on the screen. Be warned, you must do this very quickly and failure to follow the sequence of the buttons or taking to long will cause the viral detectors to alert nearby soldiers. Change into a military disguise and make your way over to the viral detectors and sabotage them. Don't worry if you fail the first time, you can attempt to sabotage it again, even if it still has detected you. Just be sure not to destroy the detectors or you will fail the mission. Once that is done, McMullan will arrive in a helicopter, only to take off moments later as walkers attack the site. You will be detected and a strike team will begin to pursue you. Destroy them or evade them to complete the mission.

  • Note: If you have low resources of RAM or weak graphics card, this might end up being impossible, as you must hit the corresponding number that is shown on the display when sabotoging the detector quicker than your system displays it on the screen. I had this problem, it was nearly impossible untill I upgraded to a bit faster/more RAM. Than it was easy because the number appeared on the screen normally as it wanted me to hit it instead of with a slight lag.

Errand Boy[]

Note: In case you have completed most of the events or have more EP, buy an area effect, along with a few jump upgrades and offensive powers.

After leaving Karen's house, head over to southeast of your location to find the hive. When you approach the roof, a cutscene shows Mercer entering the hive. Task is simple, run around the hive collecting the genetic material (golden orbs). After the fills up to half a visitor crashes in.

The Specialist[]

Karen seems to have betrayed you and reported your location to Blackwatch, since they have sent in their best, Cpt. Robert Cross aka The Specialist. Specialist Cross has several means to defend and attack you. He has a laser-guided grenade launcher, capable of firing at long range. You can tell when he's about to fire because he drops to one knee and uses a visible laser to aim at you. At close range he uses a stun baton, which you can see clearly whenever he pulls it out. Not only does it do damage, it also has a knock-back effect. Don't get anywhere near him when he has it out.

In the first phase of the fight you'll have to fight just Cross. Use ranged attack like whipfist against him when he pulls out his baton or the Musclemass ability while throwing debris at him. When he shoots at you, use your defensive shield. Flying Kicks also work well.

Second phase is where things get a bit ugly. Cross pulls out after you have managed to decrease his health and lets the infected walkers deal with you. Use area attacks like Whipfist Streetsweeper or Tendril Barrage Devastator, to deal with the infected, using Claws is also advisable. Use diveroll to avoid Cross's grenades in-case you are targeted by him (a laser can be seen when he targets you).

Cross drops in with more of his men, make sure to collect the health orbs dropped by the dead infected a. Reach critical mass and use the devastator. Doing so, kills the infected and the soldiers and if Cross is out of range or reloading (Should be easy to know since he shouts, "Reloading"), use Claws Groundspike to deal damage. You can also use the weapons of the fallen soldiers or activate musclemass and throw the debris around you towards Cross. Once you get Cross down to almost low health you will win the fight.

A cutscene shows how Mercer is injected by Cross and weakened. After this you'll be stripped of most of your powers. You can still sprint and disguise yourself however, most of your offensive and defensive powers are locked. As soon as you regain control, sprint out of the area and hide until the alert level drops.

Under the Knife[]

Dana informs you about a pathologist called, Bradley Ragland might help you. Head over to hospital at Upper East side, marked on your map. Avoid any military bases on the way. Ragland says he might be able to help if you find him a body from Penn Station (Called as "Patient Zero"). Follow the marker to the south of your current location.

Each APC with a commander is in a group of APCs. If you try to run up and hijack one of the APCs the other vehicles will shoot you and knock you off the APC. To make things hard with a disguise, there are UAV patrols along with these APCs. Grab one of the infected walking below in the streets, hurl the infected or any grabbed object towards the UAV. In-case you are detected, just drop behind the building you are standing. With the UAV destroyed,disguise yourself, preferably a military disguise and walk towards the APC who's drone you destroyed. Enter the APC and consume the commander undetected.

Drive the APC in your possession towards the new targets location. Here you have to destroy the tanks attacking the hive. You can either fire at them using the tank you brought along, or disguise and assume control of each tank. The second stealth option deals much less health damage, you can also use the disguise to blend in with the soldiers using missile launchers (Use stealth consume to gain the disguise and the missile launcher). Be careful of the hunters in the area, you can just keep hijacking the tanks to avoid them and any attention from the military.

The Captain in-charge of this assault, who is also your target sends in two waves of backup to deal with the hive. After you destroy them, he will personally arrive to deal with the situation. If your cover hasn't been blown yet, then enter his APC and consume him without a fight. And if you have been drawing the military's attention, then expect a lot of resistance.

Watch Cpt.Eric Lim's Web of Intrigue to find the location of the bodies.

The Stolen Body[]

Note: Since you do not have any offensive powers to defend yourself, it is highly advisable to purchase Groundshatter and Knuckle Shockwave, if you haven't.

There usually is an APC near the intersection, disguise yourself as a soldier (Quiet useful disguise) and infiltrate the vehicle. Drive it back to the hospital to get Ragland. escort him to the military base marked on your map.

While he gets to work on the Penn station bodies, you’re tasked with defending the lab from the incoming infected. You have four minutes to keep these mutations from crashing through the lab wall, which is made of glass. You'll notice on the top-right corner of your screen a meter labeled "Lab Wall", displaying the integrity of the wall.

Initially, a few infected turn up, you can use flykick or pick up one of the many weapons laying around you. You can also consume them if one gets near the lab's wall. When Infected are attacking the wall the best move to use is a grab and throw. This will make sure you don't destroy the wall with your own attacks. Just make sure that you don't throw them into the wall. As the number of infected increase, use Groundshatter or Knuckle Shockwave to disperse them. Most of them are killed by this attack, however a few keep coming back. Make sure to consume them (no shortage of health supplements here) as they keep lowering your health with constant attacks. While you are almost nearing the end of the timer, hunters join the party to make it more fun. (Hope you haven't touched those missile launchers!!) Grab a missile launcher and fire at them, try and avoid getting too close to them. Constant fire distracts them from the lab's wall, but in-case any infected walker decides to damage the wall, grab him and hurl it towards the hunters (cause a certain amount of damage to the hunter and might kill the walker) or just consume.

Finally Ragland decides to complete his work and asks you to escort him back to the hospital. All along the way, a few Hydras claw their way out of the ground. You can stay and deal with each one for EP or just drive straight through each one incase the APC is damaged. However you will have to deal with one of them, blocking your way to the hospital's intersection. After it's killed, drive the APC to the marker.

Biological Imperative[]

This mission is quite simple if you have a military disguise. So better get one before starting.

Get out of the tank and proceed directly to the hospital, Ragland will hand Mercer a syringe and inform him to look for a Hunter. The game will load with Mercer standing at a base.

Now change your disguise when none of the soldiers are watching you and proceed towards the marked soldier. You can consume any Marine is general in order to access the helicopter. After the memory is done playing, commandeer the helicopter and proceed towards the marked targets. Hold down the target key and use the movement keys to switch (move your Mouse PC gamers), when done correctly, you will be informed to shoot the targets. After the little training, head south towards the infected zone.

As you close on to the infected zone, a signal strength meter is displayed. Hover in this zone to find the random infected water tower. when the strength bar is filled, you'll be asked to scan. Do not fire at the tank yet, but hold down the scan button. As soon as the scan is complete, a Hunter hatches out of it. Shoot it with the firepower of your helicopter but make sure not to kill it. As soon as it is stunned, get out of the heli and use the consume button to inject the hunter with Ragland's cure.

With that done the Hunter sprints away from you, following is easy if you still have the heli intact. After running for sometime, the Hunter stops with a few of its friends. Still have the heli? Then fire at the group. If not, then you will have to use the debris in the street. Do not get close to the Hunter group, since they are bound to gangup and beat you down. Use Hunter dritnap, if have acquired it. Avoid close range combat as you'll also have Walkers to face, you can also consume a few if in need of health.

After you have stunned the targeted hunter, consume it and watch as you get all your abilities back along with two new abilities.

The Door in the wall[]

After getting our powers like the Blade and The Armor back , Alex Mercer goes to meet Dana , when Dana is kidnapped by the Leader Hunter , one of the stronger hunter that Elizabeth Greene has. Mercer just has to keep the Leader Hunter in sight. Once Mercer does that the Leader Hunter calls about 8 hunters. Supposedly the use of the Blade and Shield is advised. After killing all the hunters