Although PMU was never much of a storyline- driven game, their are still spots here and there where we see a small storyline or something rivaling the game's plot. Such examples include Buneary and Eevee in the beginning, Pat on the way to Tanren, and the story of Regice in Winden along with the small part where Ho-Oh speaks to you on Mt. Skylift. Also, the Marowak Training Dojo has it's own special adventure to it as it leads players through several different routes until meeting the final boss.
Feel free to fill this in!
The Summoning Platform and Alakazam
As you start the game, Alakazam will be relieved that the summoning worked, though you find yourself as an egg. Alakazam will give you a solution to your problem and will direct you to the North towards Destiny Cavern to choose an "avatar", or a Pokémon you will take the image of. But he first commands you to talk to his three comrades that will give you information about PMU. Alakazam then teaches you about how to speak with them (with the F Key). Talk to Dodrio and he will be delighted that the summoning succeeded, then will teach you how to run (with the Shift Key). Talk to Machamp and he will tell you that you need to know how to fight to survive in the new world. Talk to Exploud and he will yell at you before apologizing and giving a lesson of how to chat and how to select a channel (clicking the chat bar and clicking the options next to "Channel:"). He will end with telling you not to be rude before breaking the fourth wall by wondering about all these boxes and buttons.
As you enter into the cavern, you will find a mysterious voice telling you about the portal leading to a world only inhabited by Pokémon, thrilling you with the adventures and mysteries that await. It will then allow you to select a Pokémon you wish to be before allowing you to set off. When you step into the light of the crystal, dizzy and confounded, but gaining new-found energy. You then feel a cool breeze before you slowly open your eyes...
Exbel Woods and Buneary
After choosing your Pokémon at Destiny Cavern, a Pokémon calls out to you, waking you up teasingly. You wake up to find a Buneary bouncing in front of you. She will ramble on about how great the weather is, wondering why anyone would want to sleep on such a gorgeous day, before realizing you're new to the forest, saying that it's easy to tell from the bewildered look on your face. She then tells you that you're in front of the entrance to Exbel Woods, explaining that it's a home to many friendly and peaceful Pokémon like her before cheerfully exclaiming her love of the forest. She then turns back to you and guesses that you're a traveler, repeating that you're new to the forest. She'll then ask where you came from, but says you're confused but tells you not to worry about it. She then offers to show you around the forest, calling you over as she rushes towards the entrance to Exbel Woods.
When you enter the dungeon, Buneary will joke with you, asking if you've met before, before explaining that the woods lead out many different places and how easy it is. She then notices that you've never battled before and emphasizes about how you never, ever battled, before telling you not to worry. She explains how they love to practice battling and said that they wouldn't mind if you practiced as well. She'll then demonstrate how to battle before searching for an opponent. A random Slakoth will appear and Buneary happily says how perfect his timing is, making small idle chat with Slakoth. He wondering if Buneary asked the same question a couple of hours ago of how he was doing. Buneary replies that it seemed a long time ago since their last meeting. She then states that a special visitor is here and asks if she could show off some "crazy awesome battle moves". Slakoth questions about another visitor, but doesn't hesitate to lend a paw to her. Buneary then exclaims how "fun, fun, fun" the demonstration will be before calling you over and asking if you're watching her battle, invite you to come closer.
She then starts explaining the mechanics of a battle, starting out with the standard attack (F Key) and how you'll only gain half of the experience if you only use standard attacks, with Slakoth using a standard attack on Buneary (dealing 4 damage). She explains how to gain more experience by using one of your attacks (Hold A, S, F, or W to choose your attack, then F to use the attack). She'll explain that you'll also see boxes and grids for attacks, explaining that these are the range of the attacks, using some moves for examples (Tackle for close combat, Razor Leaf and Flamethrower for further ranged attacks) before asking if she was too quick on her explanation. If you select Yes, she will explain the mechanics of a battle once more, but if you select No, she will show off her Pound attack on Slakoth (dealing 6 damage). She then brags about how moves do more damage to your opponent than the standard attack, but Slakoth intervenes by explaining that moves have PP and if you run out, you cannot use the move again, stating to use your moves wisely. Buneary will then allow you to practice moves on your own, stating she'll see you down the road, wishing you luck before she walks away. But before she leaves, she talks about the items on the ground and how you can pick them up with the Enter Key. She'll explain how items are useful in situations. She then talks about signs and how they can give helpful hints and how they can be read with the Enter Key as well. She then says she kept you for long enough and leaves with a farewell, telling you to use the stuff you've learned from her.
When you get to the next floor, Buneary will exclaim how you've arrived. She asks about if you gotten the hang of using your attacks and tells you that you have plenty of time to practice. She will wish to address a couple of things, explaining how to open the explorer menu (ESC Key) and how your HP and EXP can be viewed, also noting the Belly in the menu. Teasing you about how you're getting hungry, she tells you that an Apple can replenish your Belly, or any food for that matter. She then tells you that if it empties all the way, you may faint in a dungeon from hunger. She tells you that you cannot faint in Exbel Woods and how you should keep food in your inventory for future dungeons. She then explains how you can faint by lingering on a floor for too long. She tells you how much fun it can be to stay on a floor and train, but explains how a mysterious wind will start approaching. She says that you should find the stairs when the warnings come around and get to the next floor, or else it "won't be fun at all". She then encourages you to continue training and to have lots of fun before rushing to the next floor.
When you get to the halfway point of the third floor, Buneary will call out again. She'll explain that you're on the last floor of Exbel Woods, saying you are near the ending point. She then passes on one last tip before you go towards the next floor. She'll explain that you'll find the woods clearing before talking about how most dungeons have Boss Pokémon waiting at the end. She explains that there is no exception to the rule in Exbel Woods. She'll warn you to be careful, telling you that Boss Pokémon are usually stronger than dungeon Pokémon you've faced, telling you to use your moves, items, and strategies to your advantage to defeat them. She tells you she believes in you, telling you that you'll do "fine, fine, fine". She then tells you how much she hates leaving you, saying she'll miss you, before re-affirming her previous information of the dungeon clearing and wishing you luck, delighted you came around to visit.
When you reach the Exbel Woods Clearing, Joey the Rattata will be waiting for you. He says that he heard about you from Buneary, asking if you have what it takes to beat him. He then taunts you into showing what you've learned, telling you to give it your best shot. After you defeat him, he will complain about losing, but looking past his loss and saying he got a lot of practice and admits you're "pretty strong too, for a rookie". He then asks if he could join your team, explaining about how some Pokémon will come to admire your strength and ask if they could join your team. He then brags about being a strong Rattata, stating he ranks himself the "top percentile of Rattata", saying that you and him will be unbeatable if you join forces. If you say No, he will be silent before complaining not to be mean. This will recycle until you say Yes. He then states he knew you'd say yes, bragging how it's natural for him to recruit someone as strong as him. He then states how you had no choice on the matter because he joined the team before asking. He then states you need an escort, saying he would be the best choice since he's "your newest and greatest team member of all time". He then shows the way to a hidden warp panel in the back of the clearing, saying he had enough of Exbel Woods to last him a lifetime.
Afterwards, before the removal of the Eevee NPC, you would meet Eevee, who thinks that your explanation of you coming from Exbel Woods is a lie, eventually believing you later on. Eevee also thinks your name is weird. She then explains some things, and then she says that she is going to take on Tiny Grotto.
Grassroot Town and Eevee (Prior to Eevee NPC Removal Only)
In the Inn, Eevee will confirm that she's okay, thanking Milly for her services. Milly, in return, asks Eevee to be careful next time. She then says she's off to Grassroot Town before encountering your character. She will recognize you, saying it's glad to see you again and will call you by name. She then notices you wonder about how her exploration in Tiny Grotto went and Eevee explains how frightening it was and how many Pokémon ganged up on her. She then states she fainted immediately, waking up to find herself in the inn. She then states that the inn is the best place to recover your HP and PP, as well as cure status ailments, saying Milly will take care of everything. She then leaves you, saying she hopes to see you again.
Notable Dungeon Storylines (Mt. Skylift, Marowak Training Dojo, Friendship Forest, Etc.)
Near the end of the dungeon, you will meet with Ho-oh, who states that it has been watching your progress for some time. It will approve of you completing the dungeon and fly off, leaving HM Fly as a gift for completing the dungeon.
Upon entering the dojo the sensei Marowak will give you a short tour of the premises before introducing the 3 dungeon types: Bronze, Silver, and Gold. When each Dungeon boss is defeated they will tell you that you may move on to the next dojo. After defeating Medicham and Lucario, the player must defeat the sensei who in turn congratulates you and recommends you to come back and train more some time. He also mentions that eventually you may be strong enough to battle the far away dojo, which is the Tanren Training Dojo.
Entering the building, you are immediately greeted by Phyllis, introducing you to the housing center and explaining how you can enter into your house or the house of others. He will then point out where you can visit houses (upper-left hole). He then tells you about the "/leavehouse" command, then talks about how you can edit your own house by using the "/edithouse" command. He then tells you to have fun.
The Story of Winden
There was a time long ago when Winden shared a similar resemblance to the other regions found in PMU. During this era, a vast empire was housed in the region, having full control and ownership over the land. There isn't much information regarding this empire and the kingdom excluding the fact that they were quite hostile people towards outsiders, and did not take kind to the weak or helpless.
Their hostility led to the empire's downfall when the kingdom refused to aid a helpless group of unknown entities. The queen of the empire did see potential power in the entities that could aid her own kingdom in their hard times. She ordered that her guards arrest and interrogate these unknown beings...
These entities had enough of the hostility from the queen and her kingdom. All of the beings cast their own personal curse on the land, people, and the kingdom itself to reveal them for what they truly are; Cold, Heartless, and forsaken... With their curses now engraved on the land and people of Winden, the entities disappeared... As if they were never even there.
Out of fear, the queen made a choice of of desperation to seal her kingdom from the outside world, thinking it would stop the curse... However, as time went on, the climate began to drastically change, and even the people of the empire felt as if their life and soul were slipping away...
This event led to what is seen today as Winden, the remaining remnants of the empire barely even stand to this day, and those who were once inhabitants of the vast kingdom are now only lost souls, cursed to their land for eternity. Some mask the fact that they are no longer even part of the living, still thinking that their kingdom is very much alive. However, there are very few who have embraced the harshness of the endless cold, knowing exactly what they have become, and maniacally loving every moment of it...
The Pokémon that currently resides in the main halls of the ruined castle known as Mamoswine was once the captain of the Castle Guard. Once a loyal bodyguard to the queen, he is now cursed to protect the castle for the rest of his doomed existence. Like many of the Pokémon that were cursed, Mamoswine is still convinced that he is very much alive, and that the empire had never fallen. Yet in reality, he doesn't even truly exist... Mamoswine stood guard in the halls for so long, that he is no longer even living. What holds his spirit together is unknown... It is a possibility that the captain of the guard could have been a different Pokémon before the curse, and that the curse reformed his body into a ruthless, cold-hearted watchdog...
Froslass is the queen of Crystal Castle. Before the curse shattered her mask and showed everyone what she truly was, she ruled over the empire that controlled the region currently known as Winden. She is one of the very few affected who still retains memories of the curse, and even has come to terms with her fate, to the point where she actually enjoys it! She still commands all of the lost souls in the castle. (Excluding one Pokémon...)
Before the curse, she once had Royal Guards who were loyal to her in every way, and they protected her... However, once she reformed, Froslass appointed all of the Ghost Pokémon of Crystal Castle as her true guardians (The Ghosts of Crystal Castle are the only Pokémon that remember and embrace the curse for their own personal gain).
Little is known about Regice, as it only exterminates intruders, although the player can very rarely obtain Regice's Heart Slate and use it in dungeons when it is combined to the Mystery Part.
Notable Dungeon Storylines (Winden Forest, Crystal Castle + Ruins, Etc.)
Tanren Tunnel History
All we know is that the tunnel has caved in and has now been rebuilt by a Machamp and most likely some others.
Pat and Tanren City
Tanren Training Dojo
The Closed-Off Desert
Notable Dungeon Storylines (Tanren Mines, Beach Bunker, Tanren Chambers, Etc.)
The Old Version (Winden Docks)
Notable Dungeon Storylines (Inferno Cave, Etc.)
Shortly after your encounter with Sharpedo and Crawdaunt and after you drive off the Muk, Grimer, Swalot, and Gulpin, you are able to get HM Dive, which allows you to enter the Seafloor Ruins. If you go to the stairs on Floor 20, Whiscash will be encountered, saying that he is hungry, almost mentioning he could not help but eat the food, and then battles you to see how useful he is, hoping his boss will be happy if Whiscash defeats you. Of course, you win, and Whiscash flees, realizing that he is going to be in trouble with the boss. If you are wise enough to search for the Secret Room after getting the Seafloor Key, you have a run-in with Team Razor Shell, who then fight you. After defeat, they retreat, and you go on. If you enter the Floor 40 stairs without searching for the Secret Room, you overhear a Quaqsire and a Tentacruel talking about you, such as what is in your explorer bag, but they talk too loud to the point where you finally lose your patience and interrupt the Quagsire to demand that the hidden Pokemon show themselves. Realizing that they were talking too loud, two Tentacruel and two Quagsire emerge, with the Tentacruel wanting to dance. You are able to defeat them, and they leave, with the Quagsire telling you that you have not seen the last of them. After you get to the Secret Room, you save a Phione from the clutches of Sharpedo, Crawdaunt, Kingdra, and a Tentacruel. You then fight Sharpedo, Crawdaunt, Kingdra, and Team Razor Shell. Despite being outnumbered (even if you have three other players aiding you,) you win, and the villains retreat. You move on, unaware that the villains have their insidious eyes on the treasure. After a truly long struggle to Floor 60, you encounter the villains, who are defeated, and the villains say that you will suffer the same fate. You move on, but suddenly, Kyogre appears, thinking you are a backup member. Without any method of convincing Kyogre otherwise, you fight Kyogre. Succeed, and Kyogre will get even more angry, saying that he is not done with you, and then tries to use Hyper Beam without even aiming it at the other players.
But right before your life can be ended, Manaphy saves you, and asks you if you are alright. Manaphy then explains that the same Phione you saved earlier told Manaphy what happened. Manaphy also tells Kyogre that you are not a bad guy, but an ally. Kyogre tells you that you gained Kyogre's trust, and Manaphy offers to show you the treasure. Kyogre tells you to follow Manaphy while Kyogre deals with the villains, and bids you farewell. You follow Manaphy, and Manaphy gives you a tour, even showing you the giant bubble. Manaphy then offers you a Deluxe Box for saving the Phione.
If that Deluxe Box happened to contain a Sea Dew, you gain access to Central Seafloor Ruins, where you can get a Wonder Egg from another Deluxe Box at the end. After that, you need both the Sea Dew and the Wonder Egg and locate the Seafloor Secret Chamber at floors 51-59. If you find it, you can use your Wonder Egg, where a Phione appears and, seeing you as a threat, battles you. After you defeat it, you can recruit it.