Chapter 1

After returning from their Guardian recruiting mission, a story told in the Soul Kingdom spinoffs, the Soul Princes are informed of the next plan of the Sins of True Darkness. The specifics are a little hazy, but someone important to Soul Prince lore has been brainwashed and is now targeting said Guardians. "Guess our trip around the universe isn't over yet… where to first?"

You can go after the Guardians in any order.

Precursor's Domain

Dax and Jak meet up with the Soul Princes again when they visit Precurra. They explain that the Heartless have started appearing all over Haven City, stealing Eco from the new generators. The two help them and co. "restore the generators" by storing bits of Eco in small pods. When it is shown that the generators were getting weaker instead, it is revealed that Jak and Daxter were possessed by Ira and Superbia respectively the whole time. The Sin of Pride had been able to possess the Ottsel through his small developed ego. The two Sins then use their hosts' Eco powers to transform into twisted versions of their Dark Eco forms. And with the gathered Eco, they become more powerful. Luckily, the Princes manage to save Precurra's heroes from the dark spirits and they turn back to normal. Daxter uses his Guardian powers over Light and Yellow Eco to recharge Haven City's generators before the traveling heroes leave for the next world.

Lylat System

The Soul Princes have to deal with a possessed Krystal, because Fox's existence is unknown to the Sins. Orbital Gate Assault stage in Smash used as inspiration for this segment. Murray gets to drive the Landmaster. Enough said.

N.Sanity Island

The possessed Crash, with an appearance similar to Dark Spyro, is attempting to restore the Cortex Vortex from Crash 2 using a captured Coco. I shouldn't need to tell you that would be bad.

Phantomile (Klonoa)

The Magician returns and is working with the possessed Klonoa to turn dreams into nightmares for the inhabitants.

Oddworld

The possessed Abe is making a planet already infamous for slave labor even worse… through this, the Sin here is setting up a betrayal in the resistance.

The Quilt (Nightmare Ned's area)

The mental health of Ned is in jeopardy, leading the Soul Princes to question if they made the right decision by making him a Guardian.

After checking on the Guardians, the Soul Princes use a rebuilt Continuum Jumper to go and visit other universes containing their own alternate Soul Princes.

Sweets Universe

Basically one big Wreck it Ralph Sugar Rush reference. I haven't seen the movie, so I can't comment much on this universe.

Flip Flop Universe

Role swap universe that Sly has been to before. Peach and Daisy swap roles with Mario and Luigi, Carmelita is the thief and Sly is the cop, etc.

Cyberpunk Universe

The Soul Princes investigate the universe the tech used to make Clockwerk originally came from alongside techie cyborg Soul Princes.

Princeswap Universe

Long before I got involved with Soul Kingdom, the Soul Prince list at one point had Spyro instead of Rayman, Red from Pokémon instead of Ratchet, and Crash Bandicoot instead of Sly. In this universe we get to see what it would be like if they remained Soul Princes.

Sky Universe

The Soul Princes reunite with the Portal Masters, and get an update on the current status of their army of Skylanders after helping take down the small remaining pockets of Kaos's forces.

Submerged Universe

A world entirely underwater that's home to only aquatic lifeforms, the Soul Princes help Ariel the Mercooper and aquatic takes on the other Soul Princes defeat their versions of the Sins. Subs and diving gear are heavily involved. Think Dimitri's sections in Sly 3.

Unreality

A world on the other side of the Galaxy of Hearts where Light, Darkness, and the war between them don't exist, the Soul Princes need to help end a ongoing mech war that Sora's ally Yozora is struggling with. Lots of Kingdom Hearts 4 theories used, and possibly some meta references to Soul Kingdom being a fanfic.

The Final Battle (Soul Kingdom)

The Soul Princes attempt to strengthen the seal on the Black Chaos Emerald with Bentley, Penelope, Tails, and Clank all working together to make it flawless. After buying the geniuses some time, the Sins are defeated/sealed away for good, and the galaxies of the Universe of Life start to link to each other. Happy ending. During the credits, we hear from Bentley some info on what happened to the villains just like in the Sly games.