I'm late to the party, but it doesn't matter. I'm calling this right now.
Himekawa has Alphamon as a partner Digimon. This explains why both had similar "arms reaching out" moments, why both are dark, mysterious figures, and why both wanted Meicoomon captured. Also explains why he was introduced as a villain, but not killed.
Himekawa/Alphamon were attempted to be stopped by the 02 kids, but were ultimately defeated, allowing her to continue her plans.
The 02 kids were defeated because them and the 01 kids had a falling out (which is why they went at it alone, as well as why the original kids kinda had an "oh, it's Ken. And he's evil again. Okay let's just kill him and get this over with" reaction). Basically, they're Scrappy Doo.
Ken was actually defeated and the Ken they fought was only a solidified illusion (y'all know what I'm trying to say), but he definitely wasn't the real thing. This is why Imperialdramon wasn't that strong, why Hackmon was there, and why he didn't say a damn thing the entire time.
Hackmon is the male agent's partner, and is there to record the information of Himekawa's actions in a way to prepare the Digidestined to fight her. Both are working under the facade as villains when it comes to Himekawa, but are actually against her and will eventually turn on her.
Himekawa doesn't want Meicoomon dead, but instead captured so she can control her because...
Meicoomon was infected by Himekawa through a virus she created. That virus was done to destroy the digital world from the inside, and she wants Meicoomon back to actually get things accomplished. However, the plan didn't go the way she wanted as Meicoomon was partnered up with MeiMei, which resulted in her being unable to truly spread the infections around.
Leomon being infected awakened Meicoomon's infection (by negating MeiMei's love, which was a form of treatment)
So this basically adds up to:
The Digimon being released are showing up to give Digimon a bad name in the real world. The Kuwagamon they fought were released to see how powerful the team was. Alphamon was released to finish the Digidestined off after seeing they were pretty strong. Ogremon was dropped to further the negative views. And "Ken/Imperiadramon" was a plan from the government dude to help the Digidestined train, but also one to help Himekawa "capture" Meicoomon. The Leomon infection and murder wasn't planned, which is why he was shocked and upset and Himekawa was shocked but pleased.