光博士开发了可以融合主人操控者与领航员的同步晶片，可是却被阴影人偷走了，就在科学省被异次元空间包围时，热斗使用仅存的同步晶片与洛克人双向融合，打败了野兽人。

Lan, Maylu and Chisao visit the Sci-Labs and witness Dr. Hikari's latest experiment in Dimensional Area technology—CrossFusion, the merger of a NetOp with his/her NetNavi, but the CrossFusion makes a NetOp lose his strength. However, the laboratory is attacked by real-world viruses and the Darkloid NetNavi SavageMan. Lan has no choice but to perform CrossFusion himself and stop SavageMan. After beating SavageMan, Lan passes out, but recovers a few seconds later.

熱斗はナビのデータをオペレーターにシンクロさせて実体化させる実験に立ち会うため、科学省の祐一朗を訪ねる。その時、同省では室内の空気が無くなるという事件が発生。これは謎のナビ・ビーストマンの仕業だった。