Location: Slowpoke Well

Details:
Three grunts and a boss kick off the new incarnation of Team Rocket, where they plan on selling Slowpoke meat across Johto. Follow them back to the well outside Azalea Town and put the first few to rest. They'll use Pokemon you've probably seen at this point and won't be a challenge.
The Rocket at the end of the well serves as the leader, although his team isn't any harder to beat than the others. If you have a Mareep it can get the job done on its own, though pretty much any non Grass-type can as well.

Rocket Grunt	Koffing
Battle Type Single Battle Items	Level 14
	Attacks: Tackle Smog

Location: Mahogany Town

Details:
The Rockets have been using radio waves to transmit a signal forcing Pokemon to evolve. You'll need to bust your way up to the Lake of Rage, catch the Red Gyarados, then follow Lance back to town to infiltrate their hidden base. Avoid going through the toll booth the Rockets have set up as it will be a $1000 surcharge.
Rocket's base is a complicated mess. The statues trigger trainer matches, so try and turn them off using the computer as soon as you can. You'll have to get two passwords - one for the generator room and one for the main office. Defeat different trainers and chase Murkrow around the building to get it.
In the base you'll encounter a plethora of wild Pokemon - yes, you can catch some of the Pokemon the Rockets are using in their scheme. The striped floor is home to Pokemon traps wherein you're forced to battle Koffing, Geodude, or Voltorb. As well, the final section of the base requires you to fight three Electrodes. If you've yet to add these Pokemon to your collection now may be a good time.
Boss: Male Executive #1 (Fight #1)
This executive has an easy to beat team. Featuring Pokemon you've probably already seen, the only things of concern are Raticate's Hyper Fang and Zubat's Confuse Ray. Other than that the battle should be a joke.

Rocket Executive	Zubat	Koffing	Raticate
Battle Type Single Battle Items	Level 22	Level 22	Level 24
	Attacks: Leech Life Bite Supersonic Confuse Ray	Attacks: Tackle Smog Sludge Self Destruct	Attacks: Hyper Fang Quick Attack Scary Face Tail Whip

Boss: Female Executive (Fight #1)
The nameless executive is fought on the second basement floor. If you have a Psychic-type Pokemon it will work wonders against Gloom and Arbok, though Murkrow will take no damage from its moves. Keep in mind that Gloom can put you to sleep, and Murkrow will use Pursuit to catch fleeing Psychic-types before the switch in.

Rocket Executive	Arbok	Gloom	Murkrow
Battle Type Single Battle Items	Level 23	Level 23	Level 25
	Attacks: Leer Bite Wrap Poison Sting	Attacks: Sweet Scent Absorb Acid Sleep Powder	Attacks: Peck Haze Pursuit

Location: Goldenrod City

Details:
In their most diabolical scheme yet the Rockets have taken over Goldenrod City. The trainers in Radio Tower have mostly Magnemites, weak Poison-types, and Rattata. Every Rocket Executive is fought here, however, so don't take this mission lightly.
Boss: Male Executive #2 (Fight #1)
This executive on the fourth floor is fairly straightforward. His Golbat is nothing to worry about if you have a team of on-par leveled Pokemon.

Rocket Executive	Golbat
Battle Type Single Battle Items	Level 36
	Attacks: Leech Life Bite Confuse Ray Wing Attack

Boss: Male Executive #3 (Fight #1)
This one might be trouble. Watch out for the Koffing that have Selfdestruct: even though they faint themselves, the move is so powerful it can wipe out a member of your team in an instant. Bring a Ghost-type, Rock-type, or Steel-type along to handle it. Steel-types won't be poisoned either so that's an added bonus. The Weezing is basically the same except it opts for the slightly more powerful Explosion.

Rocket Executive	Koffing	Koffing	Koffing	Weezing	Koffing	Koffing
Battle Type Single Battle Items	Level 30	Level 30	Level 30	Level 32	Level 30	Level 30
	Attacks: Tackle Selfdestruct Sludge Smokescreen	Attacks: Tackle Selfdestruct Sludge Smokescreen	Attacks: Tackle Selfdestruct Sludge Smokescreen	Attacks: Tackle Explosion Sludge Smokescreen	Attacks: Tackle Selfdestruct Sludge Smokescreen	Attacks: Tackle Selfdestruct Sludge Smokescreen

Boss: Female Executive #1 (Fight #2)
This queen bee of the Rocket pack has come back for more, evolving her team for the challenge. Arbok can paralyze you, Vileplume can put you to sleep, and Murkrow is a general pain in the backside. Employ the same tactics as before however and you should be a-ok.

Rocket Executive	Arbok	Vileplume	Murkrow
Battle Type Single Battle Items	Level 32	Level 32	Level 32
	Attacks: Wrap Poison Sting Bite Glare	Attacks:Absorb Sweet Scent Sleep Powder Acid	Attacks: Peck Haze Pursuit Night Shade

Boss: Male Executive #1 (Fight #2)
The head Rocket uses a couple of Pokemon you may not have seen yet on your second run in with him. While his Koffing is more or less the same, he brings in two of the new Dark-types - Houndour and Houndoom - to fight you with. They both share the weak Ember attack and flawless accuracy Faint Attack. Consider a Poliwrath if at all possible - Water/Fighting would be Fire/Dark's worst enemy. Finish this fight up and proceed to the Goldenrod Underground to clean up the last few Rockets, trounce your rival, and save the Director.

Rocket Executive	Houndour	Koffing	Houndoom
Battle Type Single Battle Items	Level 33	Level 33	Level 35
	Attacks: Ember Roar Bite Faint Attack	Attacks:Tackle Sludge Smokescreen Haze	Attacks: Ember Smog Bite Faint Attack

Location: Cerulean City

Details:
The last Team Rocket grunt is found in Cerulean City. He has stolen the Machine Part from the Power Plant and it's up to you to bring it back. After defeating him on Nugget Bridge, he'll inform you he's hid it in Misty's gym. From here, he'll proclaim the true end of Team Rocket, and leave for a familiar new region to settle down and have a family...