They were hit-and-run thieves, robbing and leaving...
Team Rocket wanted territory. Their interests did not conflict at all. Team Rocket would help them injure an Elite Four member, and they would help Team Rocket probe the Lightning Team's true strength. It was mutually beneficial. So what if Team Rocket got to play the fisherman?
"Boss, tell me." A Ping was very calm. After being an undercover agent for so long, he had needed to disguise himself in Team Rocket and in the Lightning Team as well. He was used to keeping his emotions hidden, masking everything beneath expressions that should not have been there.
"A Ping, we're preparing to make an example of the Lightning Team. Running into you was truly unexpected. We received news that the Lightning Team's boss was injured, so we'll make our move tomorrow. I'll notify you before we act. Pass the news to Team Rocket, and perhaps you can even claim Team Rocket's bounty..."
"Once we take out the Lightning Team, Team Rocket can move in and occupy Old Town. As one of the first infiltrators, and with another great achievement under your belt, you can easily become a Team Rocket officer here..."
"Eat from both sides. What do you think?" Yu Hai smiled at A Ping. As a double agent, if he handled things properly, he could profit from both sides.
"Alright." A Ping considered it carefully and found it feasible. He realized the Masked Pirates also had bounties on their heads, though those were not as valuable as bounties for heads and identities.
He definitely would not reveal their identities unless he no longer wanted to survive. By then, not even hiding in the League would leave him a place to stay. Being silently dragged out and knocked unconscious by Gengar was proof