Ok a couple of questions how come I cannot get into the last gym?

You need to wake the sleeping GROUDON an KYOGRE and tame them by waking rayquaza. Go to the walkthrough for the full info.

You need to defeat Archie in Seafloor Cavern and awaken Kyogre before you can get in the cave. Then after Kyogre and Groudon both are awakened, you can go to the cave, talk to Wallace, then go to the Sky Pillar, awaken Rayquaza, return to Sootopolis, and you can go in the gym.

Cave on top of the gym? You can stop thinking about that now don't worry about it, it doesnt even really exist, there is no cave on top of the gym. To get it all you have to do is go to sky pillar, which is a bit north-east of pacifidlog town and navigate your way to the very top. You may need a mach bike but I don't think so. Just walk up to the gigantic green thing, it's a Pokemon i'm sure youve heard of it, rayquaza. It will fly off. Fly back to sootopolis city, youll see some cut sequence and the two other massive pokes will leave and most things will be back to normal in the city. Go and talk to Archie and Maxie in front of the gym and they will leave, you can then enter the gym and figure out the easy puzzle you are presented with. Watch out, the leader has a kingdra with double team.

You need to get dive and go under water and stop team Aqua.

To get the last gym open, you must go to Route 128 and find a diving spot where you will find an entrance where Team Aqua is.

When you go in, you should see the submarine that Aqua stole from Slateport. Come back up to the surface and you will be in the Seafloor Cavern( you need HM STRENGTH and ROCK SMASH).

Work your way through that place and you will come to seven boulders. However, you don't have to go through those boulders. You can go around the boulders, but you will have a double battle with a grunt and a rival you already battled at the Weather Institute, Shelly.

Beat them and you will come to 12 boulders. Use STRENGTH to get around the boulders. Go through the doorway. There you will find TM 26 EARTHQUAKE.

You will then find a pool of water with a lengendary Pokemon. Walk in front of it and you will be captured by Aqua Leader Archie. Then, you will be in a battle with him, but beware! If you Have trouble defeating Archie, then you will have many difficulties defeating the last gym.

Once you win the battle, Archie will receive a message from Aqua Grunts outside. The Grunts say it's raining much harder than they imagined.

Then Team Magma will come in. They will say some things and you will be transfered outside. Steven will then be there. He sees A big storm cloud over Sootopolis City. You will then FLY to the city. SURF to the other side and talk to Steven.

He will take you to the Cave of Origin. His friend, Wallace is inside. Go visit him and he will tell you about the Legendary Pokemon, Rayquaza. However, Wallace does not know where it is. He then asks you. Select the Sky Pillar. Then Wallace will take you to the Sky Pillar, but he forgets you!

That means you have to find the Sky Pillar yourself. The Sky Pillar is in Route 131 east of Pacifidlog Town. Work your way through the Sky Pillar and walk up to Rayquaza. You won't get all the way to it, but you will awaken it.

Once you do that, go to Sootopolis City, and then Rayquaza will put a stop to the dueling Legends. Then go to the gym. You will talk to Wallace and Steven. Then... You will be able to challenge the last gym.

HOPE THIS HELPED !!!!!