The NetSavers and Lan's friends have devised a plan to bring ProtoMan back from the darkness with a VaccineChip. Luring him into a trap at a deserted hotel, the plan is put into motion, but the chip fails. Chaud performs CrossFusion with Dark ProtoMan to try and cure him, sending the two into a world of memories where they battle with the darkness. The darkness is eventually alleviated, but Chaud and ProtoMan are both hospitalized after the battle.

为了能够让布鲁斯恢复原样、科学省和IPC研发的疫苗晶片和异次元转换器一起派上用场、由热斗和洛克人亲自上场对付变成黑暗机器生命体的布鲁斯、炎山又在最紧要的关头上阵、总算将被封印住的布鲁斯找了回来…

科学省では祐一朗の開発したディメンショナルコンバーターとワクチンチップが完成。これを使ってブルース奪還作戦を実行に移す。まず、廃屋となったホテルにダークブルースをおびき出すという計画なのだが…。