– What are Methane Clathrates? –
Methane clathrates (or hydrates) can be thought of essentially as methane trapped in ice, compressed in the sea bed. They are surprisingly common. Due to this, they have been proposed as a source of hydrocarbons in the future, when oil reserves have been depleted (hence why Britannia is mining them).

– What do they do? –
If the methane is released, the bubbles of methane greatly reduce the local density of the water. Boats above that were previously buoyant suddenly fall like bricks. If there is enough gas, theoretically planes above may be affected as well. (Trivia: some people think engine noise destabilizing methane clathrates are the cause of the Bermuda Triangle disappearances)

– What happened? –
Zero ordered the Black Knights to fire upon the seabed near the mining machine, releasing the methane in the seabed (and presumably the reserves from the machine as well), causing the aquatic Knightmare Frames and ships to sink/capsize.

That said however, as Asha so eloquently put it: “Geass is a series about giant floating mechanical suits and psionic powers… think the chemistry of the bubble attack should be the least of any scientific concerns.”

Lelouch was so random telling those guys to dance and howl and stuff. Someone fantasizes too much…

I found it somewhat conincidental that a large enough…thing of methane hydrate was just in the right place for this attack. I still don’t get why methane hydrate would capsize all those ships…

I’m supposing that because the temperature in which methane hydrate is stable at is 18 degrees celsius, that the explosion of the torpedos caused the methane hydrate to become unstable, thus, creating some kind of bubbly stuff that somehow capsizes ships…

Ah the wonder of plot wholes, still nothing a compacting of the whole series into three bite size episodes will not cure along with rewrites and new animation a-la Gundam Seed style, can’t fix!!