1. The big badass Alien that slaughtered Major Strickland and his team before you left the island has somehow crawled up on the flight deck. As the soundtrack suggests, it's time for the big fight.
2. The game refers to it as the Alien Exosuit. Helena will transmit a signal through your suit to weaken it so this time, you can kill it. Missiles, Minigun or Gauss rifle can be used to damage it. But of course, it's going to take a lot of firing to bring down.
3. There will be an abundant supply of all the aforementioned weapons and ammo on the flight deck.
4. Missiles are the best choice when available since they allow you to deal maximum damage in the shortest time. Fire away all three missiles from a launcher and take cover. But since each launcher only carries three missiles, you can't rely fully on them.
5. A good place to hole up is near the door which you came in through, as this area provides much needed cover and a big stock of ammo.
6. The Alien will retaliate with a variety of attacks. The most common of them is the freeze ray. Strife away or take cover to avoid it.
7. If hit by the freeze ray, you will freeze like a statue of ice. Repeatedly press the movement keys to shake yourself free.
8. From time to time, Alien Scouts will fly in to join the fight. Take them out with the Gauss rifle.
9. The alien will slowly advance at you throwing around anyone or anything in its way. Keep the pressure on and keep firing with all you've got.
10. The Marines seems to be stupid enough to wander away from cover and run into the Alien. Learn from their mistake and try to stay in cover.
11. If you get close to the Alien, it may snatch you with its tentacle and throw you around, causing severe damage upon impact. Switch to 'Armor mode' as soon you get roped in.
12. After a while the Exosuit will get really enraged and start using these deadly energy cannonballs against you in addition to its other attacks. If you see one of these being powered up, run like hell to one side or take cover behind something big, because the cannonballs have a large blast radius.
13. It is recommended that you quick save from time to time, as you may die several times during this tough battle.
14. Note this spot with overturned vehicles and weapon crates, next to a big rupture on the deck floor. It's on the opposite side from the door, a little closer to the Alien Exosuit.
15. You will get an infinite supply of missile launchers from this crate. Not a very comfortable place to hang around now, but this spot will be very useful later in the game.
16. It's a good idea to use 'Cloak mode' when wandering out of cover looking for ammo.
17. If you want a Minigun, go to the north of the deck, away from the Alien. Staying away from the Alien has advantages, obviously. This is a great place to hole up, since the big piles of wreckage offers good protection and Minigun ammo is right in front of you.
18. This is perhaps the only situation in the campaign where you'll find a target suitable for the Minigun so make good use of it. In normal difficulty, you can actually kill the Alien with two cartridges of Minigun fire.
19. Once it has taken enough beating, The Alien will collapse and blow itself to smithereens. Cheers all around.
20. Psycho will congratulate you and bring the VTOL close to pick you up. The green marker on the radar will point to the approaching VTOL.
21. Ah, There's our VTOL. But wait! What is that monstrous thing rising from below?
22. It's a colossal Alien warship. Our troubles are not over yet. We have actually got a glimpse of this leviathan in the end of the 8th chapter where Nomad escorted Prophet out of the ice sphere.
23. The warship carries some serious fire power, such as this Singularity cannon on its wings. Luckily it doesn't target you with that.
24. What will hurt you are the four turrets which fire menacing ice shards. They can kill you in seconds so stay in cover when the turrets are active.
25. And the silly freeze ray again? Come on; it's supposed to be a warship. That being said, its best to avoid the Freeze ray as much as possible, because what follows it could be the turrets.
26. Now let's get to business. You don't stand a chance against the warship out in the open so you need to find cover fast. The best place to station yourself is behind the overturned vehicles, next to the crate with an infinite supply of Missile launchers. As mentioned earlier, it's next to the big rupture in the deck floor.
27. You'll be asked to take out the four turrets so that Psycho can bring the VTOL close to the warship, enabling Helena to hack down the shields protecting the Singularity cannons on the wings of the warship. You can identify the turrets by the glow on them when they charge up to fire.
28. Once you have located the turrets, get yourself a Missile launcher. Be sure to always keep your head down.
29. Use the scope to accurately target the turrets and fire away. Two missiles will take out each turret in Normal difficulty.
30. Destroy all four turrets, picking up new launchers from the crate as needed. It's a good idea to switch to 'Cloak mode' before poking your head out from cover.
31. Once all four turrets are down, the VTOL will hover near the left wing and Helena will start her work on the shield. At the same time four Alien Scouts will fly in harassing the VTOL. Engage them with the Gauss rifle.
32. By the time you are done with the Scouts, Helena would have brought down the shield.
33. After the shield is down, you get to use the TAC cannon that you painstakingly picked up from the Armory. Just select the TAC cannon and point it at the wing to lock on. Once it's locked on, you can pull the trigger and launch a nuke missile.
34. The nuke will knock out the wing, eliminating the Singularity cannon with it. That's one down.
35. Now Psycho and Helena move on to the other wing, and four more Alien scouts promptly appear. Same drill as before; take out the Scouts while Helena deactivates the shield.
36. After the shield on the second wing is down, destroy it with TAC cannon.
37. Now that its cannons are gone, the Warship will advance towards the Carrier and position itself above your head.
38. A small turret at the underside of the warship will start firing at you so be prepared with a Missile launcher when you see the warship advancing. Two missiles will take out this turret.
39. Meanwhile four very aggressive Alien Troopers will drop off from the Warship and start attacking you. Use the Gauss rifle to engage them. However, there is no point in trying to eliminate all four of them, as the Warship will pump out more if a majority of the Troopers gets killed.
40. Instead, focus on the blue-glowing hatch at the belly of the Warship. Keep firing missiles at the hatch while avoiding the attacks by the Troopers. You may have to keep switching between the Gauss rifle and the Missile launcher to do this.
41. Four Missiles will blow open the hatch. Then lock on with the TAC cannon and send in a nuke through the hole.
42. The nuke will blaze the inside of the Warship like a furnace, starting its death sequence.
43. Now the whacked-up Warship starts crashing down on the Carrier, threatening to sink it. Switch to 'Speed mode' and run like hell to the far end of the Carrier, to the south. The VTOL, now indicated by the green marker on your radar, will be waiting for you.
44. As you approach the VTOL, a cutscene begins and Nomad jumps onboard the VTOL. Now sit back and enjoy the final cinematic sequence of the game.
45. As the VTOL pulls away, you can see the Warship crashing down on the Carrier, then both sinking.
46. Halfway through its descend, the Warship explodes in blinding white light, at the same time pulling everything into it like a black hole. A bit of drama, as the VTOL struggles to press forward and Helena almost falls out.
47. As Nomad pulls Helena back in to the VTOL, the debris of the Warship and the Carrier plunge down into the ocean in a stunningly beautiful whirlpool.
48. Psycho cheerfully informs that he is picking up a signal from Prophet, indicating that he is alive and kicking. Now that they know how to defeat the Aliens, the team decides to head back to the island and take the fight to them.
49. The game ends as the VTOL disappears into the horizon, where the island and the Alien ice sphere is outlined by the breaking dawn. Game over.