nothing. the game is over. congratulations. (well, you can go to cianwood city and enter the cave to catch groudon and rayquaza.)
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you catch it in cerulean cave
There is no such Pokemon as "Shadow" mewtwo. There is a regular mewtwo that you can catch like any other Pokemon. It's located in the Cerulean Caves.
No you can't catch Mewtwo in Pokemon silver, you must trade it from Pokemon yellow.
You can't catch Mewtwo in Gold, Silver, or Crystal. But you can catch it in HeartGold and SoulSilver in the Cerulean Cave at Lv70.
In my opinion, it would probably have to be Mewtwo. I mean there might be harder things out there, but Mewtwo was the biggest challenge I had ever faced in Soul Silver. (NOTE: HEART GOLD AND SOUL SILVER IS BASICALLY THE SAME THINGS. THE ONLY DIFFERENCES ARE NAMES OF THE GAMES AND VERSION EXCLUSIVE POKEMON.)