Fortree City is obviously different that most other cities, proabably because this one is in the trees. There is not much here to see, however one Old Lady will give you TM10, Hidden Power, if you answer her question. You cannot access the gym, so instead continue along to the east of the city. Fight any trainers you may see, then go to the bridge. You cannot pass any further past the man for the same reason you couldn't enter the gym, so talk to him and answer yes to what he says. A Kelceon will appear, and then you must fight it. If you win, he will give you an item to detect these hidden Pokemon that are blocking your path. So now head back to the Gym. It can be confusing, but is not too diffucult. This gym is the Flying Gym, and took me quite a few times to beat. The Gym Leader, Winona, has 4 Pokemon. Her first Pokemon is a Swellow, who is level 31. He will try to use Double Team, so be sure to attack quickly. It will give 1075 Exp when beaten. Her other Pokemon are Pelipper, who is level 30. He is a Flying/Water, so use an Electric type! He will dish out 1053 Exp. Next up is Skarmory, who is level 32. He isn't that diffucult, and will give out 1152 Exp. Her final Pokemon is the hardest, Altaria. He is a Dragon/Flying type. He knows Earthquake and flamethrower, so stay on your guard. He also knows Dragon Dance, which boosts his attack and speed. I recommend trying to Paralyze it as soon as possible. When you beat it, it will give you 1152 Exp. Winona will give you her badge when you beat her, which lets you use Fly, and lets you control traded Pokemon upto level 70. In addition, she will give you TM40 and 3300 Yen.
Now that you beat the Gym, traveling will be alot easier, due to Fly. Go back to the bridge, and continue along south. It will start to rain. That means when you enter a battle, it will be as though someone has used Rain Dance. There are a few trainers scattered around, but nothing intense. Fight them all, then go on south as much as possible. Then go east. You found find some more trainers. If you need to heal, just Fly back and do so. Well, if you have someone on you that can Fly that is. Once you get past all those trainers, you will eventually reach Lilicove City! You will see a few Aqua members scattered around, however they will not fight. You will see your Rival standing in front of a building as well. If you say Yes to what he says, you will fight him, so be sure to heal before you do so. Once you look around and talk to everyone, go to the northeast part of the City, then drop down a few ledges. Go more Northeast to the Aqua member, and use Surf while going more north. When you go inside, you will see a few Aqua members blocking the path. Talk to them, then leave. Now backtrack a bit, going west of the City, back onto Route 121. You will see a platform allowing you to surf south onto Route 122, so do so. Surf around Mt Pyre, and you will eventually see a Cave enterance, and go in. This place has many Ghost types. You can go upstairs to find items, or west, so you can go outside to another area. If you go west, continue along that path. You will eventually find afew Aqua members talking to some old people. Once you fight them, they will leave. Now fly back to Slateport City. Look for alot of people standing around, then talk to them. They will clear out, and you will go inside. There, you will see Team Aqua quickly leave!
Now this building seems like it will be confusing, so I will give it its own paragraph. When you enter, battle that guy running around the water. Once you beat him, go north. You will see 2 white circles. Take the right one first and get the item, then go left. Walk along that path and fight both those trainers. Go southwest, to the circle under where you came from. You will see alot of circles here, however its a puzzle. Go to the one on the left. Then go left again, then once more. When you get the the final row on the bottom, go to the circle on the far left. You will be brought to a room with 4 items. However, the first 2 items are really level 30 Electrodes. Once you get all that, go back north using the same type of pattern, and go to the room with the 2 trainers again. Go to the circle on the right. In this room you will see another Aqua running around. Fight him and go to the south circle, and get that item. After that go back, and to the circle at the right of the room. Once there, go upstairs. Fight that trainer then go down the other stairs. Fight the trainer there, then go on that circle. You will see the shadow again, and the another Aqua. Fight him, and the shadow will leave. Go on that circle, then go upstairs, and you are back to where you started. When you leave, you will notice that the Team Aqua members have left, allowing you to go east to Route 124.
Now travel along Route 124, going east. When you reach Route 125, then go south. You will eventually reach Mossdeep City. There is nothing much in this town, but if you go in one of the houses, you will receive HM08. However you cannot use it until you beat the Gym. So why don't we head on over there. The puzzle here can be annoying, but is fairly easy. Be sure to fight everyone you see as well. Once you make it to the Gym Leader, you will notice something different. The gym match here is a Double Team! And the Gym Leaders are Tate and Liza. They each have one Pokemon, a Lunatone and Solrock. They are both Rock/Psychic type Pokemon. Lunatone looks like a moon, and is level 42. He doesn't do too much other than Hypnosis, and is easy to beat. He gives out 675 Exp to each of your Pokemon. Solrock looks like a Sun and does fire moves. He is also easy to beat, and gives 675 Exp. After you beat them both, you will get 8400 Yen, and TM04. In addition, you can now use HM08. HM08 teaches a move called Dive.