The conflict was arguably the most significant in the Syphon Filter conspiracy, since it triggered Rhoemer's assault on Washington after Gabe attempted to kill him but failed. Both factions suffered from losses: for the Agency it was Ellis, while Black Baton racked up innumerable casualties, both in personnel and assets.
Attempting to convict Gabe Logan and Lian Xing of so-called 'crimes against the government' during Syphon Filter 3, Secretary of State Vince Hadden engineers Senate hearings. The first person to testify was Gabe himself, after assassinating Chinese general Shi Hao to prevent him from acquiring Syphon Filter.
Logan's story is essentially a flashback: it tells what happened before Rhoemer assaulted Washington D.C.
Upon dropping into the jungle, Gabe takes out several Black Baton soldiers, and meets with Lian. The duo proceed into the compound in search of Ellis, destroying numerous turrets as they go, but discover he is dead: the site has also been compromised, and many patches of plants have been incinerated. Gabe continues with his tasks while taking down the opposition.