Feb 13, 2017 | 37 Comments
Crysis 3 walkthrough and complete guide
Welcome to the world of Crysis 3, a deep jungle experience awaits you in the Dystopian New York setting as you battle through hordes of CELL operatives and search for the evasive Alpha Ceph...
Note: Walkthrough written on "Veteran" difficulty setting.
You can bring on the visor using the "B" key or also hold your MMB and select the visor option.
The Visor is very important for full fledged playing of the game. In the higher difficulties it is extremely important that you use the visor in each new section of an area on a level. The basic function of the Visor is to show the locations of various things and enemies around you.
Tagging - Using the visor, you can tag enemies. To tag enemies, just open your visor and you can see the locations of enemies as triangles. All the triangles appearing on your screen are enemies. Just center your visor screen on a triangle and the Visor will automatically tag the enemy. A tagged enemy will appear as a red triangle with a white triangle inside it:
Searching - You can also search for things using the Visor. You can look for ammo caches (you can tag them just like you tag enemies) and more importantly you can also locate and tag datapad locations. The datapads look like floppy disks and you can tag them too, they look like this:
Hacking - Hacking might be the most important aspect of your Visor. To hack, just open the visor and look at a Turret or a Lock, they'll have the picture of a hand lock on them and you can hit F to start hacking:
After you hit the hack button, you'll get a wake on the screen and a hexagon moving up and down. When the hexagon (while moving) comes on the wave, hit F to lock-on to the wave section. There can be 2 or more wave sections to lock onto -
Nanovision - The nanovision is like a heat detecting visor which allows you to have a vision even when it's pitch black.
You can activate Cloak mode using "E" or use the selection wheel using MMB.
Possibly the most important mode. The cloak allows you to become invisible.
Use cloak to move undetected, the slower you move, the lesser energy is consumed. You can only fire the Bow undetected while still in cloak, any other weapon (not including grenades) will cause the cloak to disrupt. You can also disengage the cloak for a second, shoot the enemy in the head and engage cloak again. If you can do this in a couple of seconds then you'll probably breeze through the game on any difficulty.
Bring up maximum armor using "Q" or the MMB menu.
Maximum Armor causes your Nanosuit to strengthen up. This mode is especially useful when you are taking fire from enemies. The more fire you take, the more energy will be consumed in this mode.
Bring up weapon customization using "X".
This is another great mode which allows you to change the way your weapon works. From choosing different types of ammunition to different attachments for different parts of your weapons - you can make your weapons into anything you wish.
Upgrading your Nanosuit: You can do upgrade your Nanosuit when you come across certain modules while exploring during the game. The upgrading part is covered in the walkthrough itself so keep reading.
The upgrade module looks like this:
You can unlock as many modules as you want but at once you'll be able to use only four different types at once. So whichever four you keep in a sequence, you'll use them only. You can also store three favorites according you your wish and change between the settings as you see fit.
Nanosuit Training Tutorial
The basic tutorial covers the navigational controls of your Nanosuit -- jumping, sprinting and crouching.
The weapons training mode allows you to shoot at targets in different ways. It teaches you to toggle fire modes and open weapon customization to choose various options for Barrel, Under-Barrel and Scope attachments. You will also get some basic grenade throwing training. After you complete the training you can still move around throwing grenade on the targets that are still there. When you want to move out of this module then just go backwards to the waypoint.
The Nanosuit training module shows you how to use the Armor, Stealth and Visor modes. The stealth mode shows you how to make silent kills which are a critical part of you skill set while playing the game.
In the advanced training you will learn mode functions such as hacking Sentinels (which are turrets). The hacking feature is one of the most important features of the Nanosuit. Details on hacking are written in the Nanosuit section above.
The Tutorial Sandbox gives you a little piece of environment where you can test the functions of your suit live. There's a Sentinel Turrets nearby and some enemies moving around and you just have to kill them or move to the other side of the field to the waypoint to end the tutorial.
-- PROPHET --
After the intro you get me meet an old friend and you'll probably be shocked to know who it is. Anyway, follow your friend till you get to the top of a large tower and your friend leads you inside. He hands you a weapon, use the weapon customization (x) to attach a silencer and go in -
PRIMARY: Infiltrate The Libery Dome
To infiltrate the main Dome, we need to pass four to five areas which have enemies scattered. The first thing to do when you enter a new area is to put up your visor and tag all the enemies, ammo caches, Data and Blackbox locations. Do this after you pass through each door in the game and you won't miss anything.
As soon as you move in thru the door, there's a CELL operative to the left. You can stealth kill him if you are under Cloak. There ar two paths leading out of this room, one to the right and the other to the left. You should open your visor right now and tag enemies from this room and remember that you can always take one of tow options - use armor to go in directly and kill all the marked enemies or use stealth to kill them one by one and move past them undetected. You can do anything you wish. The most important thing here is to move across and into the next area.
If you leave the first room from the left, you'll come to a platform outside which is on the left side of the main room. Here at the end to the left again is a Vent which you can use -
Use this vent to get inside a room to the left and you'll come to a door which you can unlock using the keypad to it's right -
Psycho joins you here, (remember to use Visor to spot the locations of datapads). Follow Psycho and go to the next area - killing anyone if necessary. He gives you the Bow here - the best weapon of Crysis 3 (and you get it in the first mission itself). Here in this room where he gives you the Bow, you also have another Data pad. Tag enemies from this room and move out slowly. You can make silent kills from a distance using the Bow but if enemies spot the bodies of other enemies then they'll get alerted. You need to make your way to the other side of this area and climb the gangway. You'll soon reach a checkpoint and as soon as you step outside, you'll see an explosion in the distance.
Follow Psycho and he stops near a door - look to the left inside the window with your visor and hack the terminal here -
You should also tag the two datapads here and move in. Collect all the things inside and tag the next set of enemies. In this area you can either pass through on the ground or walk on top of the gangway. Go in and go through the tunnel like things. You'll come to a closed door with a lock pad to it's right -
Use it to open the door and go through. In the next place again, just tag your enemies and pass through in a manner of your desire. At the end use your visor to hack a lock to get through a gate -
You'll see Psycho in the next room and he just killed a guy who has a datapad on him. Follow Psycho into the lift to end this level.
Welcome to the Jungle
You'll know the meaning of the mission as soon as you set your eyes on the new New York.
Anyway, move ahead and if you open the Visor you'll get a read on some hardware nearby. It'll look like a pair of goggles. Go there (Psycho takes you there anyway) and you can pick up your first [[Nanosuit Upgrade Module]] -
You'll get four Upgrade points and you can open up the suit customization window using "H". Unlock and use whichever you want to - read the Nanosuit Upgrading section above to get an idea.
After you upgrade the suit, follow Psycho out and into the Jungle.
PRIMARY: Enter High Line Park
First go ahead and switch on your Visor. You'll see a land mine in the distance keep it aside for now and move to the left end of the path here and switch on your Visor. You should be able to spot a Data pad here. And also a [[propaganda poster]]. Go back and hack the mine and keep following Psycho. You'll see some Visions near a broke-down robot ahead. Keep going to Psycho and you'll come to a closed gate, break it down and walk up the stairs -
PRIMARY: Look for a weapon in Sector I-Delta-5
Move ahead and into the clearing. Always keep yourself cloaked or behind some obstacle like a wall or a bus so that you'll avoid being spotted. Psycho gives you the locations of four sectors around you ahead. The weapon will most certainly be in the farthest sector. You'll see that it's a Bolt Sniper and its a Ceph weapon. But fortunately, Prophet is part Ceph.
PRIMARY: Take out the Tower Cannons
There are three cannons on the tower ahead, shoot them one by one, cloaking and un-cloaking yourself. Go up to Psycho's position but be wary as you'll need to pass thru a land mine area again. Hack the land mine and move ahead. If you still have the Sniper then take it ahead and you'll come to an opening with enemies ahead of you. Tag all of them and kill them and keep going. Soon, you'll get a secondary objective as you move thru the area.
SECONDARY: Investigate CELL Beacon
Move to the CELL Beacon and you'll have to fight a couple of enemies there. Also you'll get a datapad which is to the left of the Beacon. If you open the Beacon you'll get a Nanosuit Upgrade Module.
Now, go to the next checkpoint as Psycho is waiting for you there. Jump down into the well using armor mode and move ahead. Keep your Visor on so that you can spot a datapad and also tag enemies.
PRIMARY: Reach the Northern Railyard through the Subway
The next few areas are just routine places having a few enemies - one has a couple of Ceph, the others just have routine enemies. You will be able to open the door leading to the next area only when you kill off the Ceph in the room. Soon you'll see yourself in another large area with enemies on the lower and upper level. There's a level below the lower area which is water logged and you can find a datapad in there. To get to the upper gangway (where the waypoint is) you'll have to move to the other end of the area and you can see the stairs leading up to the waypoint. The waypoint takes you to a zipline which leads you to the next area.
As soon as you go out, you'll hear chatter about some Stalkers roaming around.
PRIMARY: Find the Jammer and disable it
The Jammer is to the right side far ahead and you have about 8 Stalkers in the way. The best way to take care of them is to get into Armor mode and shoot the crap out of them. Once you get to the Jammer, you'll see a lockpad on it -
Use it and then head to Psycho's position. There's an AGL mounted gun here, Hack it and break it so that you can move around with it. You'll be under a short Ceph invasion. Kill the ones that are coming to you and then follow Psycho to escape the railyard. Go behind him and do what he asks you to do. You'll be on a roller coast ride from here so enjoy the trip.
The Root of all Evil
After the cutscene you team up with Psycho again and so, follow him outside to see the Dam which is a backup power generator for CELL. Move along and crouch when you come to the broken wall and go through the hole to the other side.
PRIMARY: Infiltrate and Shoot Down the Dam's Generators and cut power to CELL Defenses.
Psycho opens up an elevator door, fall in and move through to come out to a large opening -
PRIMARY: Infiltrate the Dam Control Towers
As soon as you see the chopper leave, put on your Visor and tag all the enemies ahead of you. All you need to do now is to make your way to the other side of this area while killing enemies. How you kill them is your choice, but try to go to the left side opposite end from where you start. There are some things you should pick up from here. Once you get to the building here, you can hack a Turret and then go in and Hack a CELL cache to get [[Nanosuit Upgrade]].
Once you reach the waypoint which is shown you get additional Secondary Objectives.
PRIMARY: Shut down the Hydro Electric Controls
SECONDARY: Reprogram CELL Anti-Air Units
Move out towards the waypoints and look through your Visor to see and grab anything you want to. When you reach the left most room of the building here you will find a VENT to the left of the room. If you go thru this vent and reach it's other side then it's a great Vantage Point to kill enemies -
You will find a datapad along with a JAW in one of the rooms which leads to the Dam Controls. The Dam controls are a couple of levels inside so you'll go down some stairs and reach them. Shut them down using the key pad nearby and then get out and towards the next generator. The Anti-Air defense system is also near the controls so you can activate that too.
In the building which houses the second Controls you will find a Vent outside just as you climb the stairs -
Go in through this Vent and use the Keypad here to totally Shut down the Dam.
PRIMARY: Place Explosives at Structural Weakpoint
Move up the stairs and make your way outside. The weakpoint is under the bridge so you'll need to go into the water and plant the explosives at the place -
After some commotion you'll be up on your feet again and ready for the next set of Objectives.
PRIMARY: Infiltrate CELL System-X Harvesting Facility
SECONDARY: Investigate CELL Beacon
You'll get the secondary objective when you move ahead a bit. While moving to the secondary objective waypoint, you'll encounter Intel on your way so make sure you have the Visor equipped. Go to the Secondary area and you'll find another datapad and also a Nanosuit Upgrade module here. If you can't find the two things, just use your Visor to Tag them and then get them.
Move to the Primary waypoint and you'll come to a large Iron gate. You will be prompted to hit F when near it to open the gate so open it and go in. In this area to the left end you'll find a Nanosuit Upgrade Module.
PRIMARY: Execute Operation Jack Hammer to Prevent Nexus Destabilization
Move to the waypoint which is a lift and use it. In the chamber below, you'll come across two Data Pads. Also, There are two Keypads you need to use to restore "Pneumatic Pressure to Regulation Assembly". Move to the Center where there's another Keypad and use it and then get into the lift and perform the controlled Shut Down to get the big reveal of the plot.
PRIMARY: Avoid CELL Searchlight and make your way to the park.
As usual, you should tag the enemies first before moving ahead. Psycho won't join in with you right away since he's trying to find out how come Raash and Claire went offline. Move ahead to hit a checkpoint and then make your way throught the wilderness.
When you reach the area populate with the enemy, Psycho comms in and tells you that you can get intel on his skinners. this is a secondary objective.
SECONDARY: Secure CELL intel to discover who tortured Psycho.
Make your way toward this objective, this place is important since you'll find a lot more intel along with the info Psycho's torturers. You'll come across a turret along the way, hack it for support and move ahead. If you move to the waypoint unnoticed then you can freely grab all the data. If you get there noticed then you may encounter some reinforcements who make life difficult for you.
Along the way, if you are moving to the secondary objective from the left side of the area then use your visor to spot a [[Nanosuit Upgrade]]. You'll be nearly 60mts from the secondary waypoint before you can spot the upgrade.
After the secondary is done, move towards the priamry waypoint and when you get close to the promary waypoint, use your visor again to spot another [[upgrade]] module and a datapad -
The upgrade and data are in a room inside the building which also has the primary waypoint. You should look around for that room first before you get to the waypoint.
Once you come to the waypoint, use the zipline and you'll come into the park.
PRIMARY: Approach the Ceph Mindcarrier
After you land, use your visor to spot a datapad nearby and also look at the commotion around you. Now you'll start facing some Ceph Grunts -
They are no more stronger than the average CELL opratives so you don't need to worry. But one advantage here is that Prophet can interface with the weapons they carry and use them also. Look through your visor to spot a CELL cache and go there to open it. When you get to the waypoint, you'll see System X.
After that your objective is completed, now look through your Visor again to spot a datapad nearby.
PRIMARY: Reach the CELL Nanosuit Skinning Lab.
ALong your way, you'll see several soldiers being burnt alive in bursts of flame. After you see the first burst look through your Visor and you will spot a [[Nanosuit Upgrade]] -
Move ahead and use your visor again to spot a couple of datapads and a weapon cache. Keep going to the waypoint and when you reach a closed door, it will burst open showing you what's hot around here. Move to the sides of the Scrocher and shoot into it's flesh. The scrocher can bring up it's shields to cover itself from the front but it cannot defend from the sides. Kill it and go thru the door that was just burst open.
SECONDARY: Interface with the Ceph Pinger.
You'll get a secondary objective soon as you move ahead. Move towards the secondary waypoint and be very careful while going there since there are about half a dozen Scorchers in your path. It's best to tag them so that you'll know where they are. When you are close to the pinger you can hack it and see what happens after that. Now move toward the primary waypoint and you'll be updated with a new primary objective.
PRIMARY: Find a way to bypass the Pit Defenses and enter the elevator.
Mark the enemies around here and move ahead and when you are 50mts from the waypoint, look thru your visor to spot another [[Nanosuit Upgrade]] and a datapad.
They are inside the building you need to go to get to the waypoint. Use the kepypad outside to drop open the door and then head in. Grab the two things before you go to the elevator and meet Psycho.
PRIMARY: Search the facility for a functional cradle.
As you move through each room following Psycho, you can find datapads so make sure you are constantly looking through the visor while in this level. You will also find another [[Nanosuit Upgrade]].
Red Star Rising
PRIMARY: Appraoch the Ceph Mindcarrier
Move ahead towards the waypoint a bit and you should be able to spot a [[Nonosuit Upgrade]] thought your visor and also a datapad. Keep going ahead and you will be able to spot another [[Nanosuit Upgrade]] when you are about 70mts from the waypoint. This upgrade is in a house so look around for the entrance which is from the ground.
After you interact with the Mindcarrier something strang happens -
As soon as the cutscene ends, you'll be left fighting a horde of Ceph. Switch on Armor mode and start the slaughtering. After your new powers drain, a Ceph Reaper comes by. It's tougher to kill than the normal Ceph and depending on the weapon you are using it can take some time to kill it. Use your most powerful weapon on it and keep moving around obstacles so that you can take cover. Also, take it's weapon - the Reaper Cannon after it's dead.
PRIMARY: Locate and shutdown Archangle
After you kill it, you have a long task ahead of you. Make your way towards the waypoint which seems to be ridiculously distant. When you are about 1850 mts from it you can spot two datapads in your visor. Take it and keep moving through the broke building and as soon as you come out you'll spot a Buggy -
There's a datapad to the right on some crates. Get into the Buggy and make your way to the checkpoint. Use the minimap at the bottom left of the screen to get a clear view of where you need to go and what large objects are blocking your way. The minimap is the best navigation tool you can use since watching the road doesn't lead you anywhere. At the end, you'll need to go left onto a narrow bridge -
As you go towards the end, you'll come across a blockade and several CELL. Kill all of them and go towards the waypoint which leads you into the depts of a facility.
PRIMARY: Locate and protect Claire
From where you are, turn left and you'll spot an enemy weapon cache and also a buggy below in the distance. Get to that buggy and drive to the waypoint. You'll come across several enemies but they can be ignored with the high speed buggy (hold SHIFT for boost).
As you move, you'll come to a Tanker to the left. It is shown on your minimap. Take the tanker when you can because you're going to fight a lot of enemies. Take the tanker towards the waypoint (follow the minimap) and you'll come to several powerful enemies and a closed gate. After killing the Ceph, get out of the tanker and go left and up the stairs here and you'll come to a control panel which opens the gate ahead. There are also two datapads near the stairs itself.
Go out and switch from the Tanker to one of the buggies to the left because speed is going to help out a lot right now. Again, boost throught the road ignoring all Ceph if you want to. Once you get about 250mts from the waypoint. You will come to a blockade so you have to leave your buggy and go on foot.
SECONDARY: Destroy command center area Defence Systems
You will also get a secondary objective which is to the left of the primary waypoint. Go there but be wary of the 8 or 9 Ceph prowling here. Tag them and kill them silently or just make your way to the waypoint. If you have a powerful weapon like the JAW then use it but if not stack the fuel barrels nearby close to the target and shoot them all at once.
After that go to the primary. Go to the back side gate and you will find several scorchers here. You can kill them in anyway you want. I prefer that you use the electric bolt on one of them and take their gun and use it to burn the others too. Once they are dead a Reaper also shows so kill it. Then go to the waypoint and use the numpad to the left of the gate. The gate opens and reveals two CELL solddiers guarding the gate. Kill them or go past them in stealth.
When you go around you will see that the bridge leading to the central area where our waypoint is present is drawn up. Go to where it was touching the platform and you will find a numpad there. Use it and go to the waypoint and then topside to your friends and enjoy the cutscene.
You'll come out to Hell's Kitchen, go ahead on the path and you will come to a large opening under you and the waypoint ahead on a building. Tag enemies thru the Visor here and kill them if possible -
PRIMARY: Shut Down Ceph Air Defense Battery Alpha
There's also a CELL cache here. Make your way towards the waypoint, use Armor mode when you are dropping down a long way. You can't make your way straight to the waypoint. You'll need to go left and around some debis. Here you'll also spot Liberty's head. Keep going and in the building where the waypoint is you'll also find a [[Nanosuit Upgrade]]. Move to the first Ceph Air Defense machine and destroy it.
PRIMARY: Shut Down Ceph Air Defense Battery Charlie
Move ahead out of here and towards the next two waypoint. The one to the left is Charlie. Go towards it and you'll get a secondary objective.
SECONDARY: Provide support to rebel Mortar Unit
Make you way to this waypoint and you'll spot some rebels fighting Ceph. Kill the Ceph and the rebels will provide Mortar support for you if you tag large Ceph enemies like reapers and so.
Move to the promary waypoint and at a distance of 100mts you can pick up a [[Nanosuit Upgrade]]. Go through the buldings and at a distance of 35mts in one of the broke buildings you can get a Datapad. Just go to the Battery and disable it. You will ahve reinforcements come in ahead of you. You can ignore them and sprint out of here or something like that.
PRIMARY: Shut Down Ceph Air Defense Battery Bravo
One last system to shut down. When you move out of the area of Charlie battery you can pick up a buggy from the clearing. But you will also get another Secondary here.
SECONDARY: Clear the mines around Rebel ICV
Move to the waypoint and hack the mines using your Visor to complete this. You can also grab a ride in one of the vehicles as a gunner. You will come across Ceph drop ships which shoot at you so if you are getting shot (the guns on the ICV don't really do much damage). Get out and make your way. You will get another secondary soon.
Around the area where the Ceph gunships attack the ICV you can get out and use the visor to spot a Datapad in a broken down car nearby
SECONDARY: Locate downed VTOL
This is a little distant but you can just sprint there non-stop. When you get there all you need to do is throw away some debris which has been blocking the VTOL door.
Inside the VTOL you'll get JAW missiles and a [[Nanosuit Upgrade]].
If you come across batteries like this one -
They can be tagged in the visor and Prophet can use them to supercharge the Nanosuit now but it won't last long. Make your way to the last Defence system. Disable it.
PRIMARY: Rendezvous with Psycho at the VTOL.
You'll first need to kill all the Ceph in the area below you before Psycho lands the VTOL. You can get a battery to supercharge your suit here.
Once you are in the VTOL you need to shoot enemy gunships which come from ahead of you. Be sure to target and shoot properly because if you miss too many then they will destory your ship. After you destroy all the ships, you land the VTOL for repairs. There a Gun attached to the VTOL which you can detach. Take it and shoot the
Ceph ahead and after a couple of waves the VTOL gets up to go but you face a new enemy.
PRIMARY: Kill the MASTERMIND
What you see is a Ceph Mastermind. You will see that it has a lot of projectiles which it controls and uses to attack you. There are a few Ceph weapons around here and also 3 batterys which you can use to recharge the suit. Don't use up all the batteries just yet.
To take it down you will need to destory all the projectiles which are moving around the head. Shoot them and shoot the Mastermind only when all the projectiles are destroyed. Soon it will lift you up, keep mashing SPACE to resist it. After this it get a few Ceph buddies. Use one of the Batteries to charge the suit and destroy the
Ceph. Again it will try to pull you. Now for the last time, you'll have more projectiles to destory. After this, it'll die. Make sure you are on armor mode all the time here, when you energy is depleting go behind cover and wait for the nanosuit to charge up. You can find a lot of cover in the center area and also to the left where two batteries are present. You'll need a lot of time to kill it so don't expect this to be too easy.
Move ahead to reach Columbus Circle and end this level.
Gods and Monsters
Move a bit and open your visor to find 2 data pads ahead -
Just keep going along the only path available and you'll come across another datapad in a while. At a point, a rock will fall from the top and take you further down into the labrynth deeper. Keep going ahead and enjoy the view here You'll see how deep the Ceph have infested below the ground and even see a drop ship moving ahead.
After a long time, you'll see some weapon chaches and [[Nanosuit Upgrade]] along with a datapad. This will be the first time you will be able to spot enemies. There are Cepth Grunts ahead. Tag all of them and before you move ahead, you should have laid your eyes on the explosives in the weaopon crate. You should pick up all the high impact weapons you can like the L-Tag.
Also, keep looking thru your visor to spot Ceph Weapons. The Reaper Cannon can be specially useful. Pick up and use as many Ceph Weaponry as you can since they are really more powerful than the conventional weapons.
PRIMARY: Approach the Ceph Mindcarrier
There are two mind carriers in the area ahead and a few Ceph roaming aorund. Use either stealth or armor to kill them and go to the mindcarriers. As soon as you go into a carrier, your suit will be ultracharged. After the first carrier, some Devastators come to attack you but your suit is too powerful now for them to be of any threat.
SECONDARY: Investigate CELL Beacon
The beacon is very close to the second mindcarrier. Go to it to gain some valuable firepower. Use the tank at the beacon to kill the large Ceph nearby. Then head to the second Mindcarrier and to the next task.
PRIMARY: Close the Ceph Wormhole
SECONDARY: Sabotage the Cooling Structure
The secondary task is very close to the left from where you are right now. Go there and interact with the Ceph Hologram. Then head towards the wormhole. From where you are, you will need to go to the right side and then go to the wormhole from the extreme right side platform. As soon as you reach the wormhole, the big-daddy of Ceph comes out.
PRIMARY: Destroy the Alpha Ceph
The Alpha Ceph has three arms and you are supposed to destroy these arms. Take cover the moment you come into this area and open up your visor and tag all the weapons nearby. There are also two turrets nearby but don't activate them right now.
When you shoot the Alpha Ceph in the face, it'll open up the three arms and they have a part that flashes red at this area -
It'll open up the exoskelton there and show you a red area. You need to use the JAW rocket launcher to aim and shoot at the red things. They usually go and hit the spot by themselves so you don't need to worry too much about aiming. After you take out an arm, it'll try to suck you in but keep hitting "SPACE" to resist and then a wave of enemies come by. Activate the turret for support and kill the enemies first before getting back to the Alpha-Ceph. Use the L-Tag to take out the enemies or any powerful weapons you have.
After killing them all, get back to the Alpha Ceph. There is also a tanker to the left of this area which can be a bit useful but you will not know when it'll explode because of the Alpha-Ceph's attacks and you will die in the explosion too so it's really a waste. After you destor the Alpha-Ceph's arms. The central portion opens up and Prophet shoots an arrow into it after a little cutscene.
Also, Psycho comes in here and Prophet tries to save him but....
Again, after a little commotion Prophet lands on a sattelite. Move ahead and hack it and align the satellite point the red marking in the middle of the large Ceph Spaceship and shoot.
Witness the final Cutscene as the game finally comes to an end...
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