The nasty Team Rocket is back in Crystal, this time with the same goals as GS. Among other things this includes animal abuse, forced evolutions, and even trying to recall Giovanni from his training to lead them once again. Being scattered though they have less numbers than before and aren't that potent a threat. Still, they might be too much for the ill-prepared.

Encounter 1: Slowpoke Well

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

Encounter 2: Mahogany Town

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
Encounter 3: Goldenrod Radio Tower

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
Encounter 4: Cerulean City

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...