This has probably been asked before, but replaying the original, when you catch the spy mechanic, Toby Atanwe vanishes.
Someone must have told MJ12 where Everett's home was, and it seems highly unlikely that Everett would be able to survive hidden in a nice Parisian apartment if MJ12 really wanted to hunt him down, so it's likely they're leaving him politically neutered but alive - either because they (or, more specifically, Page) want him alive or because there's no value in putting resources into killing him.
So, is it likely that Atanwe is actually an MJ12 operative but is keeping tabs on Everett rather than just going in for the kill?
Why, then, plant the bomb and risk exposure? Because Denton at this point is a clear threat, having successfully acted against MJ12 interests. He's active, not in hiding like Everett, and has nothing to lose by attacking infrastructural assets (unlike Everett whose concern would be reasserting control - direct or indirect - over those assets). Additionally, the bomb isn't intended for immediate use, so it's more of an assurance tool (leaving aside why it took them so long to detonate it). If you don't find it, it detonates at Area 51, Everett realises what happens and has the mechanic killed by... Atanwe, in doing so potentially covering his tracks and MJ12 complicity.
It seems odd that, from a game design perspective, Toby Atanwe disappears immediately after finding the mechanic. It might just be because he didn't have reactive dialogue, for example, but it seems more suspicious than that, especially with the level of detail Ion Storm put into nuanced concepts and backstory.