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Maybe drugs to weaken them physically, something the dark synchro chip later will target when damaging them. Regal can plan to use their netbattling skills alone from the base they're kept, thus them not needing to worry about moving around much on their own.
Or the drugs can be a temporary effect, maintained only through constant doses, then the damage via dark synchro chip. It would be effective, and cause them to lower their guards later so Lan and Maylu can snatch the chips.
If they are physically weak, then there wouldn't really be a problem with them sharing a room.
So CF Megaman battles Mistman and darkloids, Yuriko manages to restrain Maylu somehow to get Mistman's PET so he obeys, they beat down Lan. Yuriko gets them guided out of the tower, finding restraints for the kids along the way, then has them knocked out before the dimensional area comes down.
Perhaps a conversation with Regal before the wake up scene? Go over the basics of the plan for the group?
That could work too. Would Maylu and her mother move in with Lan and his family for the two to still be together? Or would you try separate scenes?
How do you see this story starting? Yuriko arriving at the base with restrained Lan and Maylu, the battle with Mistman and getting captured, Lan and Maylu waking up already padded?