I wonder how Baku managed to conquer the top? It seems like Macro was able to stop Leo and Hyougo from fighting... either he somehow got them on their side, or have them in a situation where if they go help Suteguma/attack Macro they'll lose the game?
Judging from Macro's reaction, the only thing I can really think of is that he's got a bomb or something... perhaps attached to the terminal? But I feel like it should be something that stops them more definitively, rather than a threat. No idea what else it could be..
edit:
Hmm, thinking again, Leo's reaction and Baku's statements are fairly extreme... maybe it's something more drastic, like a bomb that destroys the whole tower? It was mentioned that the Tower was going to be taken down before. Perhaps Leo and Hyougo are tied up in defusing that bomb, or are being held by a threat of the bomb exploding?
Another idea I thought of was maybe unleashing some sort of poisonous gas? So that no one (except Macro/Baku, who may have prepared gas masks) can go up/down the tower? The thing that bothers me about the bomb idea is that Hyougo should still be able to go to Suteguma if he really wants to, unless the way is completely blocked for him, so a gas-related mechanism fits better.
Third idea would be somehow making the two betray Suteguma, but we don't really know about their relationship to guess how that might've happened. And it seems too anticlimatic to be likely, and doesn't fit with Baku/Macro's conversation of their 'secret weapon'.