During the plot in the first encounter, after Sam defeated Ugh Zan III, he goes aboard the Sirian Spaceship, SSS Centerprice and heads off to Sirius. Apparently, there is someone who is following him, it turns out to be Croteam Bigheads riding with their Crate Bus. When Sam's spaceship gaining speed, the Bigheads decided to use Hypercrate to catch up with him. But the brake to the crate bus is out, (Probably Mental sabotaging the brake) where the crate bus crashes on impact onto Sam's spaceship, and it crash-lands in South America, Sierra de Chiappas. Sam must now find the second, backup, Spaceship left by Sirians. To do this, he must find the Time-Lock left to Mayans by the Sirians. It is located in The City of the Gods, so Sam must fight his way there.
From your starting position, dive into the lake, all the way down, until you see a rather bright spot with a Rocket Launcher. Pick up the Rocket Launcher.
Once you surface from the lake, turn right, you'll see some small terrain there, with a tree. Go there, and pick up the armor there to register the secret, although there's a Schofield .45 there as well, but doesn't count as a secret.
From #2, there's a phone booth near the corner of the terrain (behind the rocks, in HD). Go near it to register the secret, and use it if you use to make a phone call.
(HD-only)Cut down or blow up 3 trees in the starting area, before the temple, to spawn a Tommy Gun.
(HD-only)Cut down or blow up 3 more trees in the starting area, before the temple, to spawn some bullets.
(HD-only)Same as #5, to spawn more bullets. On higher difficulties, if you pick up both bullet pickups and the Tommy Gun, two Highlanders will spawn. One right of the temple, far away, and one a bit before the temple to the right, not that far.
From the temple's position, before entering, follow the wall to the left until you see some differently colored wall. Blast it with a rocket to reveal an entrance.
From #7, proceed through the entrance to discover a secret hall of fame, and stick around for a small speech and then disco music.
From #7 and #8, turn left and follow the path to the valley. You'll see some crates. Go near them to register a secret.
From #9, there's some ammo behind the crates. Pick it up, but if you do, some waves of Kamikazes (or Kleers, in higher difficulties) will spawn when you're about to leave the valley.
In the corridor followed by the crushing blocks, before going through the blocks, when facing them, turn around, and walk to the dark area, then turn left once you're in a dead end. You'll find Mental's secret room, with a few jump pads with letters on them. If you jump on any pad that doesn't glow, spikes from the ceiling will lower and lower with every jump, until you're impaled and killed by them. Jump on the pad with the letter M first, then on the one with E, then on the one with N, T, A, L. (form the word MENTAL). A wall opposite of where you entered from will move, revealing a +100 health. You can jump on any jump pad after picking up the health.
When you exit the temple, look towards the pit, on its wall on the side you're on. You'll notice a small ledge sticking out, with a Rocket Launcher. Drop there and pick up the weapon. Jump on the lower ledge with the teleport to get back.
After crossing the pit, and grabbing the first (official Rocket Launcher, you'll notice a rock on the wall to the left, sticking out. It's rather spherical. Blow it up to reveal a secret path.
From #13, follow the path underwater, and you'll find yourself near a bridge. Pass the bridge and pick up the secret health.
Before entering the final temple and finishing the level, jump in the lake and dive in until you see a brighter spot with a +50 health.
The beginning half of this map, until you enter the temple after the starting valley, is used as a part for Palenque Demo.
This level is split into Sierra de Chiappas and Catacombs in Serious Sam Xbox. Catacombs has its own music when inside and outside. One of its fight tracks is used for "Jump Over", the Serious Sam HD: The Second Encounter versus map. Catacombs also has a complete new area, a huge ramp, with weird gravity, where enemies charge in from behind the ramp and you have to fight your way through. It also has some elements from Palenque Demo.
Sam's phone call to "Blondie" in Las Vegas asking if he's ready to come out yet is a reference to Duke Nukem Forever.
The "crate bus" references the introduction which is missing from the HD port, where Sam's ship crashes because this vehicle, piloted by Croteam, crashes into it. The craft itself is a joke at the expense of Croteam's CEO Roman Ribarić, who though the English word "crate" meant "vehicle" during an interview with satirical website Old Man Murray in 2000.