I believe this is the conversation Nidhogg and HerculesKabuteri discuss when they approach the battle.
Nidhogg: Hey, Hercules, so you are here too.
Hercules: Yeah, they force me to come to support you. So what we should do?
Nidhogg: You help me suspend 2 big boss over there, leave the small as it is, then I send them all to bottle of their deck.
Hercules: Okay, I can do that. How about that big commander?
Nidhogg: Oh, leave him to Chaos, He will take care of it.
And that is the story how the opponent's board is clear-out.
To avoid your board to be clean this way, try to destroy the Hercules before Nidhoggmon appears, and when you see the green is building the digivolution source in raising area and refuse to move out, it means they are waiting for Nidhogg, so avoid to let your digimon with high DP staying in rest state. Once you let them rest, Nidhogg will send them all to bottom of the deck.
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