How do you defeat two Pokemon that are battiling?

Don't defeat them capture them use water on groudon the fire one and all out offense on kyogre the water one since I can't think of a good move to use since electric will not work.

Go to the sky pillar. You will need the mach bike. Got to the top of the tower and wake rayquaza. It will then fly off. You fly back to Sootopolice. Watch the fight. Now you can go back to the sky pillar to catch rayquaza. Continue your journey from here and beat the elite 4 with your new pokemon.

Funny... The two Pokemon are Kyogre (water) and Groudon (fire). You "beat" them by going up to Steven. Then, go into the cave and talk to Wallace. Tell him that Rayquaza is in the Sky Pillar. Then, go to route 131, which is where the sky pillar is. Go up to the top and you'll see Rayquaza. Wake him up, and fly to Sootopolis (again). You should came across the battle scene, but then Rayquaza appears and stops them. Once the little cut-scene is finished, you are now able to catch Rayquaza in the Sky Pillar. But, this time, you will need the mach bike to venture your way up. Remember the little earthquake? Well, the big part of it occured while you were in Sootopolis. Now, there are rocks and crumbly holes everywhere. To explain how to travel through it would be too much. You'll just have to find out yourself.

First of all the fire one is actually ground(check the manual)
You beat the game and go to the weather center the scientist will tell you about a drought or a heavy rainfallthen go to that place and find the terra marine cave go into the cave and you can catch the legendary pokemon

hope it works
from:pokemongirl74

You know where rayquaza is right go there and he will roar and flie off the go to sootapooles and watch rayquaza break up the fight once that is done you can go back and catch rayquaza and then beat the elite 4 and then go to the weather station and he will say if there is a drought or a never ending drizzle and he will tell you where they are.