[Start of Volume 4]
Ctholly is dead. She dies as she did at the end of the anime, having pushed her body far past the breaking point fighting the Timere. Her body is retrieved by the Winged Guard. However, they are unable to retrieve Nephren and Willem or even confirm if they're alive or dead due to the appearance of the First Beast. The Great Sage uses some "heartbeat tracing" skill to try and locate them (we see this in one of the last scenes of the anime), but the results are inconclusive.

Willem and Nephren are also dying, Willem from his old and new injuries and Nephren about to explode from overusing her venenum. On the verge of death, they are drawn into the dream world of Chanteur, the First Beast Who Laments for the Moon. This dream/illusion takes the form of Willems home town of Gomag, set at a time after he was turned to stone in the battle against the Poteau but before the world is destroyed by the Beasts. Here, Willem and Nephren get to watch the events leading up to the end of the world play out:

The Beasts are the true form of humanity. When the Visitors arrived, they transformed the Beasts into humans by shattering their own souls and using them as material. However, the number of humans increased, while the amount of Visitor soul remained constant. The spell became stretched much too thin. A  faction of the group known as True World attempted to redo the spell, using the soul of Elq Hrqstn, the last Visitor, who was killed by Lillia  (the reason why the Elq and the Poteau were fighting against humanity in the first place is because they knew humanity wanted Elq's soul to redo the spell). However, they were unable to shatter the soul finely enough because their leader, Nils Foreigner, was missing. Nils was Willem's master who taught him swordfighting, and was also an immortal being similar to but not the same as the Visitors. Without his assistance, half of Elq's soul remained intact and kept its identity as Elq, while the other half shattered into large chunks that later became the basis for the faeries.

Eventually, the day of the end of the world comes within the dreamland. Humans begin reverting to Beasts and lashing out against the world. Willem finds out that the human who became the First Beast is actually Almaria, his childhood friend and self-proclaimed daughter from the orphanage where he grew up (she's the one he's talking to in that flashback at the beginning of the anime). As she transforms, Willem strikes her down, destroying the dream world, even though he knows that as soon as he leaves it he and Nephren just going to die from their injuries.

[Start of Volume 5]
However, they actually don't die. When Willem kills Almaria, the power of the First Beast instead flows into him. As a human, he too has the potential to revert to a Beast. Though not exactly a human, Nephren takes some of the Beast into herself, preventing Willem from transforming completely.

Following the death of the First Beast, Willem and the intact half of Elq's soul, who was trapped in the dream world and is now back in her mostly-dead but still immortal body, are picked up off the surface by military vessels from the Elpis Federation, a powerful island nation within Regule Aire. However, an accident occurs while they are transporting him, and Willem's powers as the First Beast destroy the ship. Willem and Elq crash land on an island. At this point, Willem has been almost completely taken over by the Beast. The rage of the Beast drives him to destroy the world and return everything to an ashen wasteland, as it was before the arrival of the Visitors. He has just enough self awareness to think to try and jump off the edge of island, but he doesn't have enough control over his body to even try and pull it off. In this state, Willem is found by his old master, Nils Foreigner. Nils seals the Beast inside of Willem by sealing all of his memories, and also removes some of the curse on Elq's body to allow her to move around as a kind of living corpse (the curse being the curse of Seniourious that was used to kill her, which unconditionally turns anything into a corpse, even an immortal god).

Nephren also awakes on the surface. Having become half-Beast, she's now effectively immortal and the Beasts don't attack her, and since she isn't a real human, just a faerie infinitely close to one, she is able to retain her sense of self. The spirit of one of the Poteau (Elq's guardians), Carmine Lake, also appears before her, having been trapped in the dream world with Elq. Nephren is picked up from the surface by Grick and the Winged Guard. 

Meanwhile, things back at the Faerie Warehouse aren't going great either. Ctholly killed so many Timere that no attacks are predicted for the next several years at least. With no purpose as weapons, the Faeries' position is precarious. Many islands are resentful of the Winged Guard's monopoly on weaponry, and some, such as the Elpis Federation, seek to develop their own anti-Beast weapons. If the faeries lose their status as the only effective measure against the Beasts, they'll lose the protection of the Winged Guard, and will likely be claimed by the militaries of individual islands.

At the instruction of Limeskin (the big lizard general guy), Nygglatho brings all of the combat-ready faerie soldiers to Collina di Luce on Island No. 11. This includes Ithea, Rhantolk, and Tiat (paired with the sword Ignareo), as well as Lakhesh, who had just had the dream heralding her readiness as an adult faerie solider. Nopht is left behind because she lost her sword Desperatio in the battle on the airship (Ctholly took it with her when she jumped out). 

Meanwhile, with the help of Carmine Lake, Nephren is able to track Willem and Elq down. He coincidentally is also on Island No. 11. Nephren tells him of the plight facing the warehouse, but having lost all his memories, Willem refuses to get involved. Even if he wanted to remember, doing so would cause him to instantly become a Beast and lose his sense of self, so he wouldn't be able to accomplish anything anyway. Carmine Lake attempts to get Elq to come with her, but she refuses. Giving up for now, Nephren and Carmine Lake leave for Island No. 2 to meet with Ebon Candle (the black skull thing).

It's at this moment that the Elpis Federation puts their plan into action. They secretly unleash Beasts on the city of Collina di Luce, Beasts that they brought up from the surface just as they brought Willem and Elq. To prove that they too can fight the Beasts, they deploy their own anti-Beast weapon, a massive metal golem. Willem happens to see it get damaged while fighting, and sees a dying, blue-haired faerie fall out from inside of it. The reason why the golem is so effective against the Beasts is because is is powered by the energy of several faeries simultaneously self-destructing inside of it. This unrelated faerie triggers Willem's memories of Ctholly. He could suppress his memories of he wanted to, but understanding the situation Willem instead pushes past the point of no return and regains his lost memories and his powers as a Beast. Through his own force of will and the aftereffects of the seal, he is able to retain his sense of self for just a few minutes. He destroys the metal golem so that it cannot prove itself a replacement to the faerie soldiers. Willem then confronts Ithea and Rhantolk, who were also dispatched to destroy the Beasts. With only a few minutes before he ceases to be even somewhat human, Willem attacks them, hoping that by killing him, the First Beast, they will be able to cement their place as the anti-Beast trump cards. Willem is fighting at his full power, with none of his old injuries holding him back in his new immortal body, so he's basically wiping the floor with them. He hopes that by making himself their enemy, they can kill him without regret. Tiat attempts a sneak attack using Ignareo's ability to mask its user's presence, but Willem notices her anyway. As he turns to face her, he is stabbed through from behind by Seniourious, wielded by, to Willem's surprise, Lakhesh. With the sword sticking through his chest, Willem himself activates the power of Seniourious, the power to unconditionally turn god or monster or immortal Beast into a  lifeless corpse. 

It is at this moment that the author chooses to remind us of the qualifications needed to wield this true power of Seniourious:

"Explained properly, these were the requirements to use Seniorious: 
Only those without a home to return to, those who’d given up on going back to the place they wanted to, those who’d already cast away their own futures could earn the right to wield Seniorious. 
It wasn’t someone tragic. It wasn’t someone who’d surpassed tragedy. 
It wasn’t someone without hope. It wasn’t someone who’d given up on hope. 
Only those who accepted that they would never reach the future they so wished and hoped for could take the sword in hand and aim for a different future."

Following this battle, the faeries have once again secured their position. Willem's body is taken to Island No. 2, where Elq and Nephren now both reside. While the Great Sage and Ebon Candle would be able to revive Willem by weakening the curse, much as Elq was revived, there's no point since he would just come back as a mindless Beast. In the final scene, Willem sits next to the Beast inside of him, in some kind of dreamscape within his own mind or soul. His teacher, Nils Foreigner, appears before him, explaining that he has to leave this world because he overused his powers putting the seal on Willem, and that he can take Willem's mind with him if wants. Willem refuses, choosing instead to stay and try and make peace with the Beast within himself, even if it takes an eternity.

[Volume 5 epilogue]
The short epilogue is set several years later. Ithea is now wheelchair-bound, and is discussing the activities of the various other faeries with Nygglatho. Rhantolk is working as a liaison to the Orlandry Merchants Alliance, managing the warehouse's finances. Nopht is working as a part-time soldier for the Winged Guard, defending salvagers going down to the surface. Ithea remarks that she saw an airship landing earlier, and wonders if Collon and the others are on it.
 
Meanwhile, Willem arrives outside the warehouse, presumably from said airship. A young faerie named Ryehl falls out of a tree and lands on him, just like how he first met Ctholly. This faerie, who bears a striking resemblance to Ctholly, is implied to be her reincarnation. The series ends with Nygglatho tearfully welcoming Willem back. 

[Sequel series]
There's also a sequel series, SukaMoka, which has like 10 volumes out in Japan of which 3 and a bit have been fan-translated so far. It's set 5 years after the end of SukaSuka (but before the epilogue) and  follows the activities of Tiat, Collon, Lakhesh, and Pannibal as faerie soldiers. In what's translated so far, Ithea has appeared, working with the Winged Guard in some kind of espionage role, and Ryehl (from the SukaSuka epilogue) has appeared as a toddler. 

A coffin labeled "Dead Black Agate" has also been shown, which definitely contains Willem's body, but nothing has really happened with it yet. Recently Feodor, the main character of SukaMoka, had a vision of what seems to be Willem's memories, and used one of Willem's skills, but it isn't yet clear what's going on with that.