Defeat the dark mutants is a mission in The Lost Frontier. After recovering the eco seeker and returning the Phantom Blade, the crew managed to get it working with the help of Tym. Tym, who had stowed himself away on Jak's plane, explains that the artifact needs a power source before it will fully work as intended. As the item indicates the power source is somewhere across the Brink, Phoenix decides to first get supplies from Far Drop.
However upon arriving, Jak encountered several silverbacks which were terrorizing the pirate town. The owner of the supplies they needed, Barter, was only willing to part with them if they protected his stores and took out all of the mutants.
Walkthrough[]
As you head into Far Drop and enter the main square you will encounter the alpha mutant. Although stronger than the other apes, it promptly runs away at sighting you, so give chase after it. You will run into voltaic eels, which while fast and agile are not particularly strong, making them an easy target for the Scatter Gun and Blaster. Shortly after you will run into a pair of apes smashing Barter's tavern. They possess quite the punch and do not flinch easily, so use the eco amplifier power along with your new Vulcan Fury to dish out a lot of damage fast. Another pair will appear after the first two, after which Barter directs you to use the nearby aeropult.
In this area you must use your eco construct power to cast crystals, which can then be used to avoid electricity arcing across the floor. Repeat this until you reach a third pair of ape mutants at the end. Use a nearby computer console to turn off the electricity, after which you receive another eco power from the Precursor idol in the newly accessible path behind you. Eco reflexes allows you to slow down time (by pressing 
+ 
for PlayStation 2 or 
for PlayStation Portable) and move across machinery that would otherwise move at deadly speeds. After using the eco rocket jump power you will run into the alpha mutant again, which runs away as Barter orders you to go after it.
This time you will have to kill a large number of voltaic eels that are busy feeding on cabbages, which means there's a small window of opportunity for you to take them out without too much chance of counter attacks. Take out all the eels as you travel upwards along the tower, sometimes using your new reflexes power to slow down time for a platforming segment. Use another aeropult at the end to once again return to the starting area, to continue chasing the alpha mutant. Keep using your eco reflexes power to make your way through the area. At the end you will have to kill five silverbacks that are rampaging around an orphanage.
Now, after using the aeropult to return and chasing the alpha a fourth time, you will have to handle six primates trashing a crane. Use the construct power to knock two off at a time, kill them, and repeat. After taking them all out you can return to the main area to finally begin the bossfight with the alpha mutant.
Alpha mutant boss fight[]
The alpha mutant vastly dwarfs the others in terms of hit points, so prepare for a long fight. It has three type of moves. The first is a grappling attack in which it runs towards you with outstretched arms, diving in when close enough. It is quite powerful, but can be easily dodged by punching sideways and away from it before it hits you, though even if it does you can escape the grapple by pressing a series of button combo's as they appear on-screen. Note that if it misses you it will be wide open to attack, so make sure to use that opportunity.
It also possesses a number of melee strikes, namely a direct swing of the arm, a short lunge followed by a fist smashing down, and a slightly longer jump where it crashes down with both fists. The latter will cause small shockwaves of dark eco and will be executed three times in a row when it is low on health. Note that all of these moves, including the grappling attack, are purely melee, so concentrate on using ranged attacks to stay away from it as much as possible.
Finally it is capable of jumping great heights, landing at a corner of the arena while surrounded with a series of barrels that drop down from above. It will then proceed to smash the barrels, causing them to roll across the floor. At first it will smash them one by one, later two by two and as the match progresses they will proceed to bounce more and more, forcing you to dodge them by running instead of jumping over them. During all this the mutant is immobile, making him a perfect target for the amplifier, though note that the new reflexes power is also perfectly viable for use in combat to avoid the flashier melee moves.
Eventually with enough punishment the mutant ape will go down, as long as you stay aware of the fact that it gets stronger as it gets damaged, so it might be best to save the Vulcan Fury, the most useful weapon, for last to avoid wasting ammunition while it is weaker.