Meet with annihilation
Kill all foot soldiers and enemy trucks on a Meet With Enemy sequence.
On the map, there are several trucks that roam around and when you bump into one, a "Meet With Enemy" sequence starts. To get this trophy, you must kill all of the soldiers, motorcyclists and trucks at the side before you destroy the large missile truck at the back. This becomes much easier when you have the Rocket Launcher, as the motorcyclists are hard to hit with grenades and other weapons, although it is possible to achieve this using only the Revolver and grenades.
The Emperor's New Clothes
Obtain the Shin Guards, the Bulletproof Vest and the Helmet.
The Shin Guards are unlocked by completing Area 8, during the course of the story.
The Bulletproof Vest is unlocked by completing Area 11, during the course of the story.
The Helmet is found in the secret tunnel between Area 15 and Area 18. This tunnel can be unlocked by interrogating the enemy soldier in Area 19 by grabbing him with the Bionic Arm (do not shoot him!). The helmet is in the middle of the secret tunnel.
Obtain every weapon and weapon upgrade
The weapons and weapon upgrades are as follows:
Faster Than a Speeding Bullet
Block 100 projectiles using the claw.
This is very easy to get. Depending on your playing style, you might get this whilst playing through the game. If not, in any place with one enemy shooting at you, point your claw towards them and grab the bullet as it flies towards you. My recommendation is to play the game on Easy when you attempt this, as if you miss on Hard or Ultra Hard, the consequences are quite severe.
One Dozen Yashichis
Collect all twelve hidden Yashichis - one from each of Area 01 - 12.
There is one Yashichi in each of Areas 1 to 12. The Yashichi locations are shown in these videos:
Areas 1 to 10, 12:
Area 11 (2:00):
Clean as a whistle
Clear Area 02 without touching a slime blob.
The easiest way to do this is to make as little contact with the floor as humanly possible, as the slimes can't get you in the air! If a slime is coming towards you, grapple upwards immediately. Area 2 isn't that long, fortunately, and there's no penalty for quitting to the map and re-entering the level, so this shouldn't be too difficult.
Clear any of Area 1 - 12 without firing your gun.
The easiest place to unlock this trophy is Area 5, as you don't need to kill any enemies, and the boss can be killed with no bullets fired. Avoid all combat by swinging as much as possible, and going as quickly as you can. If you get held up by the flying robots, grapple them with the bionic arm, which will stall them. When the soldiers fire at you, grapple their bullets and swing past them.
Once you get to the boss, position the weak link of the caterpillar tracks as close to the ground as possible, and use grenades to blow them up. Once the driver has been exposed after you have unscrewed all of the bolts, get him to ram you again instead of shooting him - he will fly out of the front of the MAMA, ending the boss fight and netting you the trophy!
Get to the boss of Area 05 within one minute and thirty seconds.
The timing on this trophy is tight, and almost no faults can be allowed in your speed-run of this level. Go through the level and fine-tune your route as much as possible, and spend a few tries practicing it. Once you've got your route perfected, go for it, and restart if you make a mistake that costs you more than a second or so. With practice, you can execute your route perfectly and net the trophy. It might be useful to use a stopwatch for the first few attempts to time how long it takes you, so you know how much you need to improve by before you get the trophy.
This is a bit easier if you have some of the protective clothing, as then you can take damage without being delayed too much.
Don't forget to visit all of the Comms stations and make communication with HQ! You can cancel it as soon as you've connected to HQ, but make sure you do, else the door to the boss won't be open.
Part of the fun of this trophy is working out the route yourself, but if you want to know a good route, here's a video to help:
A Real Challenge
Acquire at least one star in each of the Challenge Rooms 1 - 56.
In Areas 13-19, you can unlock challenge rooms by entering one of the doors. There are 8 challenges per Safe Area, adding up to 56 in total.
Most of the challenges are quite do-able, but some, especially Challenge 56, are insanely difficult.
I would recommend trying to tackle the challenge rooms as you go through the game, as it's less frustrating if they're spaced out like this, instead of clustering them together by attacking them from the Main Menu. If you really can't do a challenge room, skip it before it starts to annoy you, as being too angry or frustrated makes the challenge that much harder. Come back to it after you've played something else.
Below are videos for all of the challenges (from this playlist
Hack through all the hacking games on Hard.
The hardest thing about this trophy is playing through the game on Hard, where it'll take only 5 shots to kill you. The hacking games are more difficult on Hard than on Normal, but if you fail them you can try them again immediately, so just keep trying and don't worry if the alarms go off. There's only 1 Comms room in all Areas, except Areas 1, 5 and 8, which have 2.
If you're going for the Elite Commando trophy and playing on Super Hard, it's worth noting that this trophy should unlock after you complete all hacking games on Super Hard as well as Hard.
Acquire all database logs.
To get this trophy you must be playing on Normal or above. Once you have got the Emperor's New Clothes and One Dozen Yashichis trophy, there are relatively few things that you won't find whilst playing through the story, which are listed below:
: Located to the far right of the secret tunnel connecting Areas 14 and 17. You must hit all of the blue switches for this to become accessible.
Here's a video:
BC Prototype Purple Matrix
: After you have found all 12 Yashichis, a door unlocks in Area 0 which leads to a room containing this item.
Here's a video:
BC Prototype Weapon
: This can be found inside the Albatross.
This video shows the location of the switch to deactivate the force-field (3:35) and the location of the power-up (2:10 and 3:40):
As long as you killed, collected and destroyed everything along the way of the story, you should have this trophy at some point during the Albatross level.
Clear the game on Super Hard.
This Trophy is a cruel, sadistic thing that will make a mockery of you and infuriate you to the point of seeing red, but it looks incredible in your Trophy collection.
To unlock Super Hard, you have to complete the game on any difficulty level. Playing it through on Hard is best preparation for Super Hard, and it allows you to complete all hacking games so you don't have to worry about them on this playthrough.
Super Hard is difficult because you die in two hits, enemies are extremely aggressive, take more hits than you, shoot diagonally, throw grenades at you, drop down platforms if you're below them, and the bosses are harder to beat as well.
The key to beating Super Hard is to avoid enemy fire at all costs. Do not get hit. After playing each area it's possible to find ways of avoiding gunfire, but if you see a bullet coming towards you, avoid it or grapple it. Comms stations are extremely useful, as they're the best way of restoring your health when you complete the hacking games.
Due to the large numbers of enemies, it's wise to avoid "Meet With Enemy" sequences as much as humanly possible. The trucks seem to move in a non-random way on the map, so if you accidentally hit a truck and die, pick a different route when back on the map, and the truck shouldn't follow.