One of the main gameplay elements that affect the ending of Oddworld Soulstorm is saving Mudokons. You will need to save at least 80% of the Mudokons to have enough quarma to get the best story ending. The main challenge of this platformer is beating every level with the fewest number of deaths, including enemies, so try to play as passively as possible.
The Monsaic, Ruins, and Blimp make up the first three levels of the game. Each stage has a certain amount of Mudokons that you need to save. Fortunately, these stages are the tutorial levels of the game, so it is not hard to rescue most of the Mudokons found in them.
Monsaic - Stage 1
The Monsaic is the first level of Oddworld Soulstorm, and there are 300 Mudokons that you need to save in this level. Fortunately, all 300 survive automatically, so you do not need to worry about finding all of them. Just play through the entire stage to save everyone.
The Ruins - Stage 2
This level will be the first stage where it will be a struggle to keep every Mudokon alive. You do not need to save all 200 in this level, but you will need to keep at least 160 alive. Play through the stage until you get to the final part, where the Mudokons will be climbing to safety in the background.
The challenge for this stage will be Sligs running out onto platforms to shoot escaping Mudokons. To save as many Mudokons as possible, place IEDs on every platform where enemies appear. Then, use your chant ability to possess the Slig in the top right corner and use their gun to shoot the other Sligs.
Once most of the Mudokons make it to the next level, explode the last Slig or knock them out and tie them up.
The next level will be a little more challenging. Some of the Sligs will have rocket launchers, so make sure you kill them quickly. The same idea for killing Sligs from the first part applies here. Place IEDs on the platforms where they run out and then possess a Slig using their chant and gun down the other Sligs. If you fall below the 160 Mudokon survivor threshold, you will need to restart.
The Blimp - Stage 3
There is only one Mudokon that you need to save on this level. The single Mudokon is hiding in a hidden area halfway through the stage. As you go through this stage, look for the entrance pictured above.
Once you go into the secret area, you will find the Mudokon. Use your chant to open the portal, and the Mudokon will teleport to safety.
That is everything you need to do to save more than 80% of the Mudokons in the first three stages of Oddworld: Soulstorm.