Part 1 and Part 2 can be read here and here.
Toal's storyline is considered the the real one, because his ending sets the stage for Ys I more thoroughly than the others, and has the longest, most involved ending sequence, but it doesn't stand alone as well because Yunica and Hugo's actions are missing the context from their own stories. We only know what's going on because we've already seen them in previous playthroughs.
For most players I would suggest the playing order to be Yunica, Hugo, and finally Toal to get the whole story, but if only two playthroughs can be stomached, skip Yunica because Hugo and Toal's stories compliment each other. On the other hand, if only one playthrough is in the offering, do Yunica, because she's self contained (and it's impossible to play Toal without finishing one of the other two).
From a gameplay perspective Toal's playthrough works rather strangely.
Since Toal is not part of the search party like Yunica and Hugo, he doesn't begin the game at the bottom of the tower like they do. Rather, he starts at the summit as one of the Darklings and when the villains learn that the twin goddesses and the Black Pearl they carry have entered the tower, they split up to capture them.
Toal is then teleported to the bottom and has to fight his way back to the top while searching for the goddesses, who he claims don't mean anything to him anymore. After all, Toal has accepted a demonic element into his soul, and is now part-demon.
The game handwaves the fact he's killing all these monsters, who are ostensibly on the same side as he is, by letting Toal say he's been given permission to kill them so he can absorb their powers. This allows for essentially the same game structure as playing Yunica and Hugo, with minor changes.
For instance, there is one item that Toal never gets a hold of for plot reasons, so he can't use it to solve the same puzzles. The game makes sure to provide an alternate means of achieving the same goal in times like those, but these alternate routes only appear on Toal's playthrough.
Toal also frequently fights different mid-bosses than Yunica or Hugo. Battles where they would typically fight a Darkling are frequently replaced by members of the search party. Toal even fights Hugo twice.
The early part of Toal's storyline makes him a hard person to get a hold of. He's stand-offish and says very clearly, on no uncertain terms, that he is an enemy of Ys. He's thrown away his knighthood and he is now loyal to the Darklings. Toal is quite vehement about it, whether he's speaking to Darklings, the search party, or even the goddesses.
But funny thing is, even though his delivery is spot on, nobody is buying it. The search party is certainly put off and hostile for a while, but they are reluctant to give up on him, and the Darklings consider him suspect no matter how good he is at following their orders.
As the player, it's hard to figure out what's going on in his head. We don't know why he turned and became part-demon, or what his ulterior motive is, if he even has one. Since Toal doesn't share his real thoughts with anyone in the first half of the game, most of the story comes through flashbacks that play after major boss fights, where we get to see what Toal was like when he was one of the Holy Knights.
We learn that as a knight he was well liked by the people who met him, even though he rarely visited his family, which makes sense since he was disinherited for joining the knights instead of accepting his place as his father's heir.
Toal was particularly close to the goddesses, especially Reah, and he was the one who had given her the harmonica she carries. It's clear that even though nothing improper happens between the goddess and her knight, they both care deeply about each other.
When he finally catches up with Reah in game, she deduces that Toal's plan is to absorb enough energy through the demons he kills to merge himself with the Black Pearl and then destroy it, because it is the source of all the demons (as well as all the magic of Ys). She has a plan though that will not require Toal's sacrifice.
Unfortunately, it quickly becomes apparent that it will require one of her own, and it's at this point in the story that Toal's facade begins to crack, with Toal and Reah independently racing up the tower to stop the other from making the sacrifice. It's rather sweet, even though Toal is canny enough to be upset that she talks about not wanting his sacrifice when she's about to force him to accept hers.
There are side trips along the way. He meets Hugo, who is not quite as arrogant and angsty in Toal's storyline, and he meets Epona as well, which results in funny exchanges where she pretends to not be interested in Hugo, even as she's pumping his older brother for personal information about him. I love that Toal ships the two of them together.
Yunica probably fairs the worst in Toal's storyline because he didn't really know her back on Ys. Toal served under Saul Tovah, Yunica's father, so he was aware of her, but he didn't know her personally. When she shows up, she comes off as a mostly passive girl who can't really fight against him, and is even found lying unconscious at one point, due to a trap she successfully navigates on her own playthrough.
She feels a little extraneous to Toal's story, more than Toal did in her own, because he could blend in with the other villains, but she sticks out as more significant than other members of the Ys search party even though she is the least ranked among their knights.
When Toal finds the other goddess, Feena, he manages to pull Reah's plan out of her and learns that the two goddesses plan on sacrificing their wings, the source of their divinity, to seal the demonic essence of the Black Pearl. Doing this would cause the two goddesses to enter a sleep that could last for centuries.
The strange thing about this story is that hearing Feena's words is what convinces Toal of what he needs to do, which implies that becoming a Darkling and destroying the Black Pearl by merging with it was never a grand plan of his. Toal is described as a bit short-sighted and stubborn, so I'm not surprised that he didn't have many details for his poorly contrived undercover work, but it's not clear why he would have agreed to become part-demon in the first place, and unfortunately that's never answered.
Further up the tower, Toal meets Reah again and this time drops his evil facade entirely to try to convince her that the sacrifice of either of them is completely unnecessary and that he's found a different way, but he doesn't get a chance to explain his plan (or if it was a lie to trick her out of the sacrifice) before they're discovered by the Darklings, who capture Reah and reveal that they've possessed Hugo.
Now that his true allegiance is out in the open, Toal is quickly forgiven by his former enemies, the search party, who help him up the tower. Unlike Yunica and Hugo's finales at the top of the tower, where everyone else shows up at their backs, the search party holds off various Darkling bosses for Toal so he can progress to the summit, and even Epona pitches in to try to help him bring Hugo back to his senses (it goes over better than in Hugo's storyline since Epona lives), which results in Toal facing the Darkling leader, Dalles, almost entirely alone, except for the goddesses.
As was hinted in previous storylines, we learn in Toal's that the reason the goddesses took off without telling anyone is because they suspected there was a traitor among the Six Priests of Ys, and that's how the demon infestation got out of hand. That traitor reveals himself after Dalles's defeat in Toal's storyline only, and it's Cain Fact, head of the Six Priests and the father of Toal and Hugo.
Cain Fact had engineered everything, including getting both his sons implanted with demonic elements to see how they can augment the human body (and this in turn ties into why Hugo and Toal have descendants that do not look entirely human in Ys I and II). Cain merges himself with the Black Pearl becoming Darm (the last boss of Ys II) and Toal fights him not with the claws he's been using since becoming a Darkling, but with his Cleria Sword which he had left behind after the battle where he'd become a martyr (and in turn this sword is the one that Adol uses for the last boss fight in Ys I, ironically to defeat Toal's many greats-grandnephew).
The battle between Toal and Darm takes so much out of Toal that at the end of it, he's unable to stop Reah and Feena from undertaking their ritual to bind the demonic essence, and it's an emotional kicker knowing how much Toal cares for Reah. Though I know she's trying to tell him how much he means to her, Reah does a really good job of driving in the painful reminders that this is really good-bye for them.
For the audience that has played Ys I we know that it will be 700 years before Reah wakes, and by then Toal will be long dead.
The epilogue covers the remaining story bits to line Ys Origin up with Ys I. Toal leaves his Cleria Sword at the foot of the Roda Tree where Adol will find it 700 years from now, and Hugo and Yunica decide to stay behind on the surface instead of returning to Ys (so they can become the ancestors of the characters Adol meets).
Toal himself returns to Ys to become a priest in his father's stead. It seems a little surprising at first that he wouldn't stay on the surface as well since that is where they entomb the Black Pearl and the sleeping goddesses, but his decision makes sense. Hugo never wanted to be a priest, and Toal had only given up his position because he thought Hugo was more suited to it. And Toal wants to work with the other priests to lay down the story of what happened to future generations.
In the final epilogue scene, we see him send down the six Books of Ys, which Adol will find many years later.
It was a good ending, and even though I'm disappointed that not everyone's own storyline is canon, Origin is one of the best prequels I've ever played. All the nods to the original story and how things came to be were spot on and never felt forced. Best of all, it feels like it could work even for players unfamiliar with the Ys series, because the references that do existed aren't shoehorned in there for the sake of being present. They're all made part of the story.