-( Story related, cannot be missed )-
At this point in the game, you should be aware of what the final boss is, or at least an idea. So, yeah, you'll be facing off against Cyber-Errol operating one of the Dark Makers. After escaping the ship and reappearing back on the planet's surface, you will hop into a vehicle and chase after this big guy. The first phase of this final fight involves you taking apart the massive creature's legs. You will find, around the feet, dark eco crystal joints. The requirement for this phase is to destroy these by shooting at them (and some of them can be quite frustrating on their own, being on the front of the foot). If I remember correctly, you will have to shoot 14 crystals, like two or three to each foot, to finish this off. There's not much to this part aside from him shooting out cluster bombs to impede or actually hit you, or a spinning top that can/will damage you if you run into it or it into you. The only thing I can suggest is to take use of the boosts that the cluster bombs provide upon defeat, boost ahead of the stubborn crystals you have left, and try to turn around and shoot them before it takes off. This beast has a large stride per leg, so it might be frustrating.
After you cripple it, all that will remain is a stacking pyramid. Take out the little creatures using whatever means you want to unlock the pistons that will elevate you to the next level, repeating the process until you get up to the very top. This is the boss fight to end this challenging game, so get ready to use your knowledge against him. I don't remember the name of the weaponry, so I apologize in advance for the rest of this. Take out your yellow Eco gun, third powerup, and shoot it off to quickly clear the three tendrils that will start each phase (and there's four for this big guy). After this, you will need to clear away the little runts that gather. Should you successfully clear the platform off, he will start shooting at you with a laser that trails you. Just keep a steady pace and you shouldn't have trouble with this. After that nostril blast, he will end up using a sweeping laser to clear the deck and expose his weak spot, the Dark Eco canisters attached to the back of its head. One well-placed shot there will take down his health by a quarter and start the phase all over (with some added spawns and trailing lasers to add spice). Rinse and repeat the strategy to avoid his attacks and clear the platform, and eventually you will finish it off, Jak-style.
*If you need to heal, use Light Jak's regeneration and then quickly return to normal. The Eco wells open up during his sweeping laser attack so that's a good time to refill if you used any.