Prototype Guide - Walkthrough
Before getting started, acquire the Whipfist Power, Street Sweeper, and Flying Kick Boost upgrades, as they are essential to defeating the boss character encountered during this mission. If you lack the EP needed to purchase these upgrades, destroy the military bases and hives in the city until you have amassed enough. The Airdash Double and Airdash Boost upgrades would be of use too.
When you're prepared, make your way to Karen Parker's lab at the north end of Central Park and hit the yellow marker there to trigger a cutscene.
Mission Objective: Collect Genetic Material
Follow the blue marker on the mini map to reach the nearby Hive. Hit the blue marker on top of the building to enter the Hive. Once inside, Sprint around and collect the Genetic Material until a cutscene is triggered.
Mission Objective: Defeat Specialist Cross
The Specialist is outfitted with a laser-guided missile launcher and an electrified baton; both decidedly deadly weapons. He is quite agile too, and can dodge most attacks, making him a formidable opponent indeed.
The key to winning this fight is to keep your distance. If you try to battle the Specialist up close, he'll equip his electrified baton and zap a large portion of your health bar. The two most crucial upgrades here are Flying Kick Boost and the Whipfist Power. If you do not have both of these, acquire them via the Upgrades menu now. Be sure to equip the Whipfist Power at the start of the fight.
Use the Whipfist Power to strike the Specialist from afar.
With the Whipfist Power equipped, you can attack the Specialist from afar, keeping out of range of his severely damaging electrified baton. Flying Kick deals a fair amount of damage per strike, and can be made even more effective through the Flying Kick Boost upgrade. Be careful however, because if you try to hit the Specialist with a Flying Kick while he has his baton equipped, you'll get zapped
The ideal time to get a hit in is while the Specialist is aiming his laser-guided missile launcher. When you spot the green laser guide from this weapon, lock-on to the Specialist, jump up into the air, use Double Airdash to move in closer, and then hit him with a Flying Kick to knock him to the ground. Immediately upon landing, lock-on to the Specialist and hold the X/Square button for a few seconds to charge an attack. A fully-charged basic attack with the Whipfist Power will knock off a large amount of the Specialist's health if it connects. He is quite adept at dodging, but if he immediately crouches down and equips his missile launcher again, the attack should connect. Be warned, however, as you can still get zapped by the electrified baton if he has it equipped.
Flying Kick can be used to hit the Specialist even while he is not aiming his gun, however there is a chance that he will equip his baton before the kick reaches him. Try to avoid going in with a Flying Kick head on; always use Airdash to get behind or above him.
Also use Whipfist when the Specialist crouches down to use his laser-guided missile launcher. Flying Kick works particularly well, however, because as you are in the air, you can use Airdash to dodge the missiles he fires off, and then move in for the attack. To use Airdash effectively, lock-on to the target while gliding through the air and press RT/R2 while pushing the Left Thumbstick/Analog Stick in the direction you want to dash. If you've acquired the Double Airdash upgrade as well, Glide for a split second at the tail end of the first and then perform the second to get the most distance. Try to fly behind the Specialist, and then hit him with a Flying Kick while he is vulnerable.
Hit the Specialist with a Flying Kick or a charged Whipfist strike when you hear him call out 'Empty!' or 'Reloading, Reloading!' because he will enter a reloading animation, leaving himself open to attack.
Specialist Cross is vulnerable while aiming his laser-guided missile launcher.
Keep your distance from the Specialist while he has his baton equipped, and continue to hit him with Whipfist and flying kicks while he is aiming his missile launcher.
Once you've knocked off about a quarter of the Specialist's health bar, he will briefly retreat, and a flood of Evolved Infected will enter the Hive. This is when the Street Sweeper upgrade becomes particularly useful. The Infected that enter the Hive will make a beeline for you, but with the Street Sweeper upgrade, you can easily keep them at bay. To perform Street Sweeper, first press X/Square with the Whipfist Power equipped, and then press and hold the Y/Triangle button to perform an elongated sweep of the space in front of you. Killing the Infected in this fashion actually serves as an efficient way to replenish lost health, as they yield red EP orbs when defeated.
When the Specialist rappels back down into the Hive, immediately turn your attention back to him. Go about attacking him in the same way you were before the Infected arrive. It may be a bit tougher now, as the lock-on system can get a bit sketchy with so many targets to choose from. The Infected serve as a distraction as well as a means of replenishing health; if you're critically low on health, Sprint Grab one of the fat Evolved Infected and consume in one of the far corners of the Hive.
With about half of his health bar gone, the Specialist will call for support. Several soldiers will rappel down into the Hive, each equipped with a weapon. These guys can be a bit of a problem, but the weapons they bring down into the Hive can be of use if you can get your hands on one. The Grenade Launcher, while rather inaccurate, can deal a fair amount of damage with a direct hit.
Weapons dropped by the military are quite effective.
Be careful when using a gun against the Specialist, as he will equip his electrified baton and enter a frenzied state. While in this state, he is very quick and can dash across the floor to swing the baton at you. So, if you manage to pick up a weapon, stay in the air while attacking him; jump up and Glide away from him if he gets too close.
While guns are effective, because things are so hectic in the Hive, it may be best to just keep attacking the Specialist as you were before.
Beat the Specialist within an inch of his life to trigger a cutscene.
Mission Objective: Kill or Evade the Military
While Alex has lost his powers, he retains his movement upgrades. Kill or evade the military (the latter option is definitely the better at this point) to complete the mission.