In Halo 3:
The Flood land on Earth via High Charity.
How did the UNSC clean up or contain the contamination? Given its past record, even on advanced Forerunner worlds the parasitic organism wasn’t easily contained or extinguished without the “nuclear” option, if you catch my drift.
The Flood never landed on Earth via High Charity. High Charity slipspaced directly to the Ark without going through the Earth portal - you see this in the mission where it appears above the Ark, opening a new portal.
For the Covenant cruiser infestation, the UNSC didn't. The Elites did, as shown in the closing cutscene to the Floodgate campaign. According to Admiral Hood, the Elites gassed "half a continent".
ADMIRAL HOOD: You, shipmaster, just glassed half a continent. Maybe the Flood isn't all I should be worried about.
SHIPMASTER ELITE: One single flood spore can destroy a species. Were it not for the Arbiter's counsel, I would have glassed your entire planet.
