Pastoria City is home to the Great Marsh, where many rare Pokémon can be found, though it will require multiple visits on separate days to see all of them. Pastoria is also home to the Scarf Guy, who lives in the house nearest to Route 213. The Scarf Guy checks a Pokémon's condition to see if it is worthy of a Scarf. If the Pokémon's condition is at its maximum value in an area, he will give out the corresponding Scarf to that Pokémon. If not, he will tell the player to improve its condition with Poffins.
Go to the westernmost house to meet a woman who will give you a Berry once a day. These Berries will notably be the ones that reduce the damage of supereffective attacks on the Pokémon that holds it. Notably, the Charti Berry that you can receive from her is a good Berry to use when making Poffin for raising a Pokémon's Beauty stat and is recommended to use for evolving Feebas into Milotic once you've had time to grow plenty of them.
If you want to catch a lot of rare Pokémon, you should visit the Great Marsh at the north end of town. For 500 you can explore the Marsh until you throw 30 Safari Balls or walk 500 steps, whichever comes first. You won't use your Pokémon to battle here - if a wild Pokémon appears, you can throw Mud, Bait, or a Safari Ball. Bait lowers the chance of the Pokémon escaping, has a 90% chance of lowering its catch rate. The mud does just the opposite, making the Pokémon easier to catch, has a 90% probability of causing its chances of fleeing to rise.
For 100, you can look through the binoculars in the upstairs room of the entrance building before a Safari Game. They show wild Pokémon in the Marsh area where they can be found. This is useful for spotting the rare Pokémon that are randomly selected each day.
Before you enter the Gym, you will be challenged to a battle with your rival.
As you will quickly figure out, this Gym specializes in Water-types. Grass- and Electric-types will do well here, but you shouldn't use Fire-, Rock-, or Ground-types. The strongest Pokémon here is level 37, so make sure your team is leveled appropriately before challenging the Gym.
The puzzle of the Pastoria Gym may appear complicated at first, having to raise and lower the water level by stepping on buttons in the correct order. In reality, there is only ever a single path that you can take at any one time without going back the way you came. To reach Crasher Wake (the Gym Leader), go down the entrance stairs, turn left and go up those stairs. You will reach a yellow button. Hit it and the water level drops. Turn right, down the stairs, and go through a narrow passage. There is another narrow passage before you reach some stairs. Climb up to the top, and hit the green button. Climb down and follow the path to another set of stairs. Battle the Sailor there, and hit the blue button. Follow the platform to the first yellow button and head right, past the stairs to the Tuber. Battle him, and follow the path right to another Tuber. Battle her, and go on forward. You will eventually find a green button. Hit it, go down the nearby stairs, and hit the yellow button. Go up, then down to the lowest level. The rest is simple; follow the path to a set of stairs, climb up, and hit the blue button. The path to Wake is clear.
Wake leads the fight with Gyarados, who has Intimidate, so lead with Special-based attackers. It knows Wake's signature move, Brine. Brine does more damage if its target has less than half of its HP left, so be wary and keep your Pokémon healthy. Waterfall will do the most damage and may cause your Pokémon to Flinch. However, one good Electric-type attack will take it out. Next up is Wake's Quagsire, whose Ground type makes it immune to Electric-type moves. Grass-type attacks are this Pokémon's nightmare, particularly Special attacks due to its weak Special Defense. It has Rock Tomb which can slow you down, but it doesn't know Brine. Yawn can be annoying, because a Pokémon hit by it will fall asleep on the next turn unless you switch it out. Chesto Berries as held items can be useful in this situation. Last up is his star Pokémon, Floatzel. Floatzel is very fast, and can hit pretty hard, but its defenses are quite low. It has Ice Fang to counter Grass-types, as well as Aqua Jet, a Water-type version of Quick Attack. It too is packing Brine, so stay healthy during the fight. A fast Electric type like Jolteon or Raichu with a good move like Thunderbolt will do well here.
After defeating Wake, you'll receive the Fen Badge that lets you use Surf outside of battle, as well as TM55 (Brine).
After earning the Fen Badge, you'll meet up with Barry again. When Wake leaves the Gym, it turns out that Barry's earlier claim that he's Wake's apprentice isn't true - Wake won't take him on as he believes neither of you need any tutoring. After this exchange Barry mentions a Galactic Grunt with a bomb near the Great Marsh's Observatory Gate. When you meet Barry and Wake at the entrance to the Great Marsh you'll find that the Grunt sets off a small bomb in the Great Marsh as a field test, and you'll from have to chase after him while Barry keeps people out of the Great Marsh until Wake can be sure it is safe.
Head through Route 213 (you'll encounter Looker there), chasing the Grunt east. Feel free to battle trainers and collect items along the way, especially the hidden Heart Scales in the sand that can be used to teach moves. You will have to come back later with Surf and Rock Climb to pick up everything.
After talking to the man in the hotel lobby and healing up, chase the Grunt all the way to the Valor Lakefront, where he'll finally give up and you can challenge him to a battle near the entrance of Lake Valor. After defeating the Grunt, you will meet Cynthia and your rival again. He briefly interrupts her to report that the damage to the Great Marsh is not as serious as expected, and Cynthia states that she is worried about the group of Psyduck on Route 210. She gives you SecretPotion to cure them of their headaches, and will then tell you the legend about a mirage Pokémon that lives inside the lake.
You can't access Lake Valor proper just yet... So why not go to the Seven Stars Restaurant where you can partake in a number of Double Battles? You will also find a lady who has lost her Suite Key, and asks you for your help finding it. Go near the entrance to the hotel and use your Pokétch's Dowsing Machine to find and return it. Much like Route 213, some of the items will require the use of HM03 (Surf), and HM08 (Rock Climb), which you can use outside battle only after defeating the fifth and seventh Gym leaders respectively.
Now that Cynthia has given you the SecretPotion, talk to the Psyduck that have been blocking access to the north half of Route 210. Administer the SecretPotion and the Psyduck will move off. Cynthia will appear and give you the Old Charm, asking you to deliver it to Celestic Town. Long grass grows rampant throughout this route, preventing the use of your bicycle. This area is a popular place for Ninja Boys to hide. Further north, the grass clears to give rise to thick fog. To ease travel, HM05 (Defog) may be used, although this is not required.
Head north through the large patch of long grass, but make sure you find all three members of the Ninja Trio and defeat them, as they won't challenge you unless you stand right next to them. Grandma Wilma, a Move Tutor, lives in a house on the northern, foggy stretch of Route 210 although you'll need Rock Climb to reach it. Previously, she lived in a famous city of Dragon Tamers, and is able to teach the move Draco Meteor to any Dragon-type Pokémon with high Happiness. Turn west, then head up the stairs and across the first bridge. From there, carry on straight, across two narrow bridges to find the powerful TM30 (Shadow Ball). Backtrack, and head south over the second wide bridge and then follow the path west to Celestic Town.