The gang down the road to Mahogany City when all of a sudden Pikachu feels sick, then Togepi. Ash starts to wonder what's going on, but he thinks it's probably just a thing that comes and goes. Then some bug Pokemon drop in near Misty, however, they appear sick too. As for a Sandshrew and a Oddish as they come out. They all wonder what's going on. The gang reaches to the Lake of Rage and try to see if there's anything about the lake that could be doing this. Then all of a sudden the red Gyarados appears from the water. This startles everyone in two ways, first because it's a Gyarados, and second because it's red. After moments of glimpsing at the Gyarados, it fires out a Hydro Pump towards Ash and company, which misses.
Soon a group of people come by, which at all don't look too friendly. Ash notices it's Team Rocket and the main person simply laughs wondering what a bunch of kids are doing. He sends out a Fearow to take care of them and Ash releases Totodile. Just before Totodile can do anything, he goes tired all of a sudden but not the Fearow. The Fearow goes in with a Drill Peck but just before the Pokemon can hit, a beam fires towards the Fearow and the one responsible was a Dragonite and a trainer. Seeing this, the Rockets decide to flee. The trainer takes them to another part of the forest around the lake and Ash thanks him. Misty notices that the man is Lance, the same Lance in the Pokemon League. They all wonder what he's doing in a place like this and comment on their progress of becoming a Pokemon Master. One last thing Ash mentions is to help the Red Gyarados, which immediately Lance says no. He explains that it would be too dangerous for Ash, after all these Rockets are no ordinary Rockets. Ash protests, but Lance still gives the no.
Somewhere else along the forest around the lake stumbles Jesse, James, and Meowth, groaning about their next meal and win. Meowth notices something in the distance that looks like a building. With a building, there's got to be some food around there they can swipe. The building however is a Team Rocket HQ, and inside is the man from before who addresses himself to a superior, Professor Shiranui. This other major Rocket in particular is Tatsumi, assigned to capture the famous Red Gyarados. Upon further inspection of the security systems, Jesse, James and Meowth are caught on camera. After walking in a hall, they fall for a trap that seals them in a hallway behind two walls of bars. Then Tatsumi comes by only to see who exactly are they. Jesse, and James say they're a part of Team Rocket obviously but a flunkie comes by to say they're not anywhere on the roster list. Jesse and James negiotiate for a while and convince Tatsumi that they're the important ones. (I don't see how they pulled that off) Just one ticket to a free meal.
While the gang walks along the road to Mahogany once more, Brock tries to talk with Ash. However Ash seems like he can't stand there and wait for things to go good. He wants to help the Gyarados, whether or not dangerous.
Back at the base, a boat's getting ready for the operation to begin. Just behind one of the docking hangers, Lance hides and waits for a chance. An unsuspecting Rocket walks by and Lance grabs him, takes his uniform and goes onto the boat disguised. Back on the boat, Prof. Shiranui explains that Project R is about to begin, but he needs a couple of "expendable" Rockets for the first part of the job. Tatsumi knows the perfect ones. He goes over toward the mess hall where Jesse, James, Meowth, and Wobbuffet are stuffing their faces and he says that they get an "important" assignment, find the red Gyarados. Everyone assembles on deck, Jesse, James, and Meowth are off to find the red Gyarados. When they go down there, they all start to argue about this whole Gyarados thing. Soon enough, an angry red Gyarados comes towards them and Jesse, James, and Meowth swim off back to the boat, where all of them break surface. As soon as the target is on sight, a Rocket handling a net gun fires it and surrounds the red Gyarados and Jesse, James, and Meowth! Prof. Shiranui gives a signal and a power shock is delivered through the netting, shocking both Gyarados and the Rockets.
The boat starts to go with the catch but Ash and company comes just in time on the scene and he sends out Totodile, Misty with Poliwhirl. They both swim to the net, Totodile chomps the net and Jesse's hair, Poliwhirl trying to rip it. Lance notices them being their and thinking Ash is crazy. Seeing the two Pokemon, Shiranui sends out for another device, which back at the HQ, a giant Radar sends waves out towards to the area. Soon Totodile and Poliwhirl get tired and let go of the net. Ash realizes it's something at the HQ that's doing this. They start to go over there.
Before anything can happen, Tatsumi catches them and hands them over to the hands of Shiranui. Ash demands what's going on and what are they going to do with the red Gyarados. Shiranui explains the whole conscept behind Project R, short for Project Revolution. The whole idea was that the Gyarados is had a strange property in it that made it red. The aim of Project R is to force Pokemon into evolving or try to achieve the "red" state. Thus, the whole Rocket faction gets a army of evolved and above-average Pokemon at their disposal. Later Tatsumi congratulates Jesse, James, and Meowth for their work, but it seems he has other means for them.
The Gyarados is later loaded onto a truck which Lance is on, along with Tatsumi and Shiranui. Leaving the lake, and Ash behind...

Thanks to Xeno Lugia for writing This for us