This walkthrough is written by Rage Quitter 87.
When you first play this mission, you'll see a little cut scene of your character running forward and cutting open a cage who has a prisoner inside (this prisoner doesn't count on your prisoner list by the way) Your character will then see Allen Jr. a few feet in front of you and your character will run towards him, but then the ground will give way and your character will fall down a pit! Allen Jr. will start laughing as a couple of enemy soldiers join him in chuckling away. It seems Allen Jr. has turned traitor.
This mission is mainly set underground and you will be fighting new enemies who are exclusive to this mission. Like the last two missions, you can use the Metal Slug you can find in the third part against the boss.
Part 1 - Entrance
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 You'll fall downward when you start this mission until you eventually hit solid land. As soon as you do, two bats and two humans with bird masks will rush towards you. These bird men use primitive weapons such as axes or will throw fire sticks at you. The bats are small and can move fast but are easy to kill. Move right and you will see a small ditch, and a platform with prisoner (031) on it. Free him and he will give you a turkey. If you shoot at the bottom right corner of the trench, you will free prisoner (032) who has a Flame Shot for you.
 Continue right and more enemies will appear, shoot them with the flame shot. You will then see a pit, jump across it and the screen will lock. Lots of bird enemies will appear, shoot them all and the screen will unlock. Now position yourself to the right side of the pitfall so about half of your character is standing on thin air and the other half on solid land, and jump and shoot upward. Card 037 Hyper Vulcan will fall out on your character.
If you have Cards 050 Weird Ruins and 054 Ancient Soul, you can access the top part of the level. Skip to  for information there.
 Continue right killing enemies as you go until you see a prisoner above you on a large platform. This is prisoner (035) and he has some canned food for you. Now go right again until a message on screen going GO!-> You'll see a torch nearby, shoot at it and an Enemy Chaser will fall out, collect it and then move on to the next section.
 To be able to go to this hidden section, you'll need Cards 050 Weird Ruins. When you have those, you will see a large platform has appeared just after the pit where Card 037 Hyper Vulcan was. Jump on the platform and it will rise.
When you can see a platform to the left of you, jump across to it and shoot upward. First a few bananas will drop down, and if you keep shooting Card 016 S.G. Clip will also drop down. Now fall back down to the platform that took you up here and it will rise again, this time ride it all the way to the top. When you get to the top, shoot at the torch and prisoner (034) will appear who has a Heavy Machine Gun for you.
 Keep going left and a bird mask enemy will attack you, kill him and crawl left to see prisoner (033) who has Card 041 Crawler+, which is very useful. Keep crawling left and there are lots of maggots in the way, stab at them to kill them but watch out for poison gas. Once you've got past them, if you have 054 Ancient Soul,
you will be in a small area where you can stand up. Shoot at the skull to reveal Card 024 I.Lizard+ and then at the ceiling above for Card 036 L.5 Armor. Now go back the way you came and continue the mission as usual.
Part 2 - Cavern
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 Go right and an enemy soldier will run on and throw some of those rolling bombs, and I've quite often seen him kill himself with his own weapon. Once he is dead, go right and the jump down a platform and shoot at the dent in the left side of the wall, prisoner (037) who will give you Card 008 H.M. Clip. Now jump up a few platforms until you can see a few enemies, go onto the same platform as them and kill them. Keep going right until you see a box, this has a Drop Shot in it.
You will also see a tied up prisoner above you, this is prisoner (039) who will give you another Drop Shot. To rescue this prisoner you will probably end up falling down to the bottom level of this area. Simply go left and jump up a few platforms to be back where you were before. Very near where prisoner (039) was, there is another tied up prisoner to the right of him. This is prisoner (040) and he will give you Card 033 L.2 Armor.
 It's very likely that you fell down to the bottom of the level when rescuing the above prisoner. Good. When you are at the bottom, go to the far right of the level, and you will see a upward spray of purple poison gas. Directly above this spray is a hidden prisoner. Throw a grenade at where the tip of the poison spray is and prisoner (042) will drop down, who has Card 071 Tarma. Now go to the very far left of this area and shoot at the bottom left corner to get prisoner (036) to appear, he has a Super Grenade to give to you. Make your way back up the platforms and go right, but this time fall down the first pit you see.
You will appear in a little area with a rocket launcher soldier, kill him. You will see a hole in the ground you can fall down. Shoot above this hole and prisoner (038) will drop down, who has the Card 017 Grenade Clip. Now drop down to the bottom level of this area and work you way back up to the top and now go all the way to the right, keep going right until the screen locks. A lot of bats will attack you, but if you duck these creatures will not be able to hit you and will fly right past you. Once the screen unlocks, go left and jump up three platforms to prisoner (041) who has a turkey for you.
 Now go back to where the bats were, and go left and go down the hill until you can see a small platform with a box on it. Jump over to this platform and shoot the box, which has Card 001 Stealth inside it. Now go all the way back to where the bats were and go right to end this part of the mission.
Part 2a - Secret cave 1
This secret area will open up when you get Card 053 Cave Maze. After the rolling bomb soldier, jump up a platform and a previously sealed off section will be open to you, go through it to be in a small room. Inside here are several bird mask enemies. As soon as you enter this section, jump forward and crawl through the gap, throw a grenade to kill the enemies on the other side. Free prisoner (044) who has Card 056 Coin, once you save him, jump up and aim at the corner to the left of the gap you just had to crawl through and shoot, Card 004 Paper Thin will drop down. Now crawl back through the gap and when you are near the exit to this secret area, aim up and shoot and prisoner (045) will fall down who has Card 059 Blue Jewel for you.
Part 2b - Secret cave 2
After you exit secret area 1, jump up a few platforms and go left and you will be able to go through another area which was sealed off previously. Inside here make your way to the far left to prisoner (043) who will give Card 075 Madoka. Shoot at the top left corner of this area and Card 002 Marsnium will drop down. Many bird mask enemies will appear once you get to the prisoner in here, so be careful. Once you have killed them all, exit this section and finish this part of the mission.
Part 3 - Underground river
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 As soon as you enter this section, move right and throw as many grenades as you can at the tall enemy tank in front of you can to destroy it quickly, then kill the soldier who is pushing a Metal Slug. If you don't kill him in time, he will push the tank into the sea so you cannot use it so kill him quickly. Get inside the tank and move right, killing many enemies and jumping platforms as you go.
 At one point the screen will lock and you will have to face LOADS of those rocket throwing divers. I hate this bit of the mission, it goes on for far too long in my opinion. Once you kill the last diver the screen will unlock so you can move to the right again.
 After a short while of going right, the screen will lock again and lots of yellow enemy soldiers will drop down. The first wave will try to knife you but if you are in the slug they cannot hurt you. The next wave will throw grenades at you so kill them quickly. There will then be another wave of grenade throwing soldiers, kill them quickly. The screen will then unlock at this point so move right and you will see a single enemy soldier with a rocket launcher. Kill him and continue right to end this part of the mission.
Part 4 - Boss
The boss of this mission is called the
Kaladgolg and is a train type thing. It has a large super laser in the middle and it's extra weapons are two mini guns and two mine launchers. At first the boss will use it's mini guns to try and get you, just jump around to avoid their fire. After a short time the guns will stop and the Kaladgolg will fire it's extremely powerful super laser, be sure to be out of its way when it fires. It will fire the super laser twice in a row. Also, the boss may fire a few mines before it fires the laser so watch out for those.
The only area of this boss you can shoot is where the super laser powers up. You can still use this Metal Slug against this boss, if you still have it, so use it's vulcan cannon on the super laser to damage this boss quickly.
When the boss is damaged, flames will be all over it. It now fires mines that float around the floor, and moves around faster so make sure you are ready to move when it does. Some of the mines contain Rocket Launchers, so if you're out of grenades and ammo, be sure to destroy them. Keep shooting the super laser and eventually the boss will blow up and mission 3 will be completed.
To defeat this boss quickly, collect the Super Grenade from part 2 and have the Metal Slug from part 3. When you get to the boss, jump out of the Slug and fire every Super Grenade into the bosses' weak point, followed by all of your grenades. If it still isn't destroyed at this point, jump into the Metal Slug and fire it's shells into the weak point (make sure you do not have Card 040 A.P. Cannon turned on for this boss) or use the Slug's vulcan cannon if you cannot get accurate hits with the shells.
Click maps to enlarge them.
The prototype has a lower lip right of the cliff at its first stall point, and has no overhanging platform.
There are invisible platforms you can jump on that nearly get you to the top ledge, but not quite...! These were likely a temporary measure until the elevator was operational, as they don't line up with the off-screen platforms that are still in this prototype (as well as the walled-off chunk).
The natives' axes are discoloured, and their melee attacks have no hitboxes; they tend to strike while on top of you, rather than within axe range. The bats are also a lot slower, less tenacious, and incapable of harming you.
The log platforms in the second area are placed differently, often with only one log, making them a lot shorter and more cumbersome to climb. There's even one positioned in a slope, but that just means you can fall through the gap.
The poison gas and leeches cannot damage you.
The two chambers (normally sealed until you get the Cave Maze card) are open by default, and the passage to the Slug Mariner is still accessible!
Background tiles for the doorways that seal off the two dead-ends can be found off-screen; the prototype already has sprite replacements sitting in the data, with slight graphical differences, plus an unknown third door. The final would remove those background chunks from the map data.
The platforms at the end of the second area are positioned higher, seemingly making it impossible to get onto them. They also have different collision; their left cliff faces are treated like walls, and there are invisible walls on top of them to the right. It's tricky if not possible to get onto them without hacking, but they revamped their collision and positions for the final.
There's no stall point of bats at the end of this area.
The top-right passage is blocked by an invisible wall, but was raised in the final to put it out of reach. The prototype is missing a card hot spot.
The hanging column was shortened in the final.
The Slug Mariner entry dock just changes the backdrop, but the exit dock was totally reworked for the final, even though it would never be seen...!
Even the unused underwater passage was changed slightly in the final! The prototype curves down slightly at its midpoint, but remains straight in the final. The prototype also has no rocks, only lots and lots of mines in slightly different arrangements than they are in the final.
Though only the back half of this area was restructured for the final, its enemy layouts are pretty different; the Sarubia is missing from the start, and so is the shield soldier pushing the Metal Slug into the pit; the Slug is just sitting before it.
The rest of the area relies heavily on shield and bazooka soldiers, and might be the only place in the prototype where blue soldiers are seen. No stall points are set up yet, and there's no assault of frogmen or knife soldiers like there are in the final.
The area has a rock ceiling (seen in some early footage), with gaps mostly over pits and where enemies drop down from above. The ceiling was removed entirely from the final version, seemingly because it does more harm than good, with your character frequently bonking their head on it and not getting full height from their jumps.
Another boss that exists as a non-interactive animation loop. The track at the bottom is positioned higher in the prototype. Walking right will take you to Mission 4.