Finally, we've made it to Mt. Moon. Before we continue, it will probably be a good idea to buy more Pokeballs from Pewter City. If you've been following this guide, you've only got 5 or 6 left, and there are at least 5 more pokemon we'll want to catch before we make it to the next pokemart. From now on, you'll want to keep a handy helping of ten or more on hand at all times. This is also the first area that gives most players trouble, so stock up on Potions if you need to. If you've visited the museum in Pewter City, you'd know that both Moon Rocks and Clefairy are said to have originated from the moon, and fallen to Earth in this very location, we we'll keep our eyes peeled for them. Also of previous note is the man on the phone we overheard talking about Team Rocket at Mt. Moon as well as any of a few miscellaneous trainers talking about new pokemon in the area.
Once inside, head up and take an immediate left past the first outcropping. You'll immediately see an item on the ground, so pick it up to find TM12. It has Water Gun, which would be extremely useful in this area, except the only pokemon that you may have that can learn it is Squirtle, which naturally learns it at level 15. Tuck that away and head straight up to find a potion in the corner, then face the Bug Catcher nearby. He just has a Weedle and Kakuna, so deal with him easily.
Continue straight and you'll find a sign that warns you of Zubat's Leech Life, and standing next to it is a Lass. She wields the prize of this place, a Clefairy, and it can do some good damage with it's sing-pound combo, so take it out quick. Head up and to the right when you can, and go down the ladder. In the first level basement, there's nothing but ladders and wild pokemon, so head down and to the left to reach basement level two. Head straight up and you'll be ambushed by the first member of Team Rocket. He has a Geodude, Rattata, and Zubat, but you can deal with those easily with fighting type moves for the first two and a thundershock for the last one.
Now that we're on the bottom floor, keep a look out for Clefairy and Paras, since they're both much more common down here. Head to the right of the rocket grunt and you'll find an HP Up on a small raised section. There's nothing else here, so head back up the ladders to the first floor. To the right and follow the wall down, you'll find another Bug Catcher, this one with two Caterpies and a Metapod. Defeat him, then head down to the left to find your first Super Nerd. He has two new Pokemon, Magnemite and Voltorb. They're both electric, so stay away from using water pokemon. Grass is good against them, as well as another electric pokemon. The other option is using Geodude or Sandshrew, as ground and rock do well against electric. After dealing with him, pick up the potion at the left.
Head back to the right. You probably noticed as you passed the second Bug Catcher some items to the right, and we'll pick those up now. The first one is almost at the bottom, and you'll find your first Rare Candy. This special treat will instantly level up any pokemon you give it to. It's best to use these immediately after a level up, so you don't waste any experience from between levels. Though it's also recommended not to give too many to any one pokemon, since they also lose you any EV stat bonuses. Further above, pick up an Escape Rope. If you're in a pinch and need to get out back to the pokecenter near the entrance quick, you can use it. Further up, take a left near the top to find the second Lass, who has an Oddish and Bellsprout, both level 11. Stay away from water types and you'll handle her easily.
Continue left, and turn down when you can. You'll shortly find a second ladder, so climb down, and again continue until the next ladder. Take a couple steps to the right and another Rocket Grunt will challenge you. He reveals a little more about Team Rocket's plans before challenging you with a Zubat and an Ekans. Watch out for Zubat's supersonic and you'll defeat him easily enough, then claim the TM01 on the platform above. Check the boulder to the right for a hidden Ether. After all of that, we can head back up to the first floor.
Back up top, head a little down, and to the left you'll be spotted by a youngster. He challenges you with two Rattatas and a Zubat, though at level 10 none of them should give you real trouble. Deal with him, then head up and left in the next area. You'll see a hiker standing in front of the last ladder, and he'll fight with two Geodudes and an Onix. Defeat him with fighting or water moves. Before heading down the ladders, go to the top-left corner and you'll find a Moon Stone. With all items collected and enemies defeated, you're ready to head down the last ladder.
Down and to the right, head down the ladder at the other end. To the right and down the stairs, there's another Rocket Grunt for you to face. He's got a Rattata and Zubat, each level 13, so shouldn't be a problem if he doesn't confuse you with supersonic. After defeating him, head up the stairs at the right. Continue around the side, down, all the way to the left, and then up. If you're playing Red or Blue, you'll face your final Rocket Battle here. He has a level 16 Raticate which can really tear up your team with it's Hyper Fang, so watch out.
• Red/Blue: Team Rocket
Continue up and you'll see another trainer standing in front of two fossils. Before you face him, go down the slim path to the right. You'll reach a dead end, but investigate the wall and you'll find a hidden Moon Stone. After collecting the hidden stone, head up to face the Super Nerd. He demands you stop because the fossils are his, and battles you to keep them both. He has a Grimer, Voltorb, and Koffing, all level 12. He'll be a decent fight, so make sure to use a few potions if you need before facing him. His Grimer packs a punch with disable and pound. Voltorb isn't too bad as screech doesn't pair well with electric attacks, and Koffing is very limited.
Defeat him and you'll get to pick your choice of the Dome or Helix fossil. For this guide, we'll pick the Dome Fossil. Head to the left, and you'll see the ladder leading to the exit below. If you're on yellow, you'll face the final battle here, so make sure to heal up before heading down. They'll stop you, demanding the fossil, and give a shortened version of their infamous Rocket rhyme, then attack you before you can do anything else.
• Yellow: Team Rocket
Jessie and James
After defeating Jessie and James, if you're playing Yellow, you should be just about done here. Make sure you've collected all of the items, most notably the two moon stones, and battled all of the trainers you'll like. After leaving, the rockets will abandon Mt. Moon so you can't catch any battles you missed with them. Also, make sure you have caught all of the new pokemon around: Zubat and Geodude are very common and common, respectively, on all floors, but are most common on the first floor and basement 1. Clefairy and Paras are both easiest to catch on the bottom floor, though still fairly rare. We'll want two Clefairys before leaving, since we can trade one later for a rare pokemon. After you've settled everything in Mt. Moon, head for the exit towards Celadon City.