After defeating kyogre in Pokemon red rescue team what shoud be done?

Well, my personal opinion is to keep exploring the dungeons that you have not completed. However, I think that if you can (as I'm not sure he will be back if you return) you should go back and recruit Kyogre.

His Recruitment rate is 50% and his size is 4 stars (remember that your team cannot exceed 6 stars in size)