Genesis spends a good deal of time -- Chapters 6 through 11 -- discussing the "mabul mayim", a flood that killed all humanity outside the ark. Here is what the Torah's text says about the universality of the flood:
ה וַיַּרְא יְהוָה, כִּי רַבָּה רָעַת הָאָדָם בָּאָרֶץ, וְכָל-יֵצֶר מַחְשְׁבֹת לִבּוֹ, רַק רַע כָּל-הַיּוֹם. 5 And the LORD saw that the wickedness of man was great in the earth, and that every imagination of the thoughts of his heart was only evil continually. ו וַיִּנָּחֶם יְהוָה, כִּי-עָשָׂה אֶת-הָאָדָם בָּאָרֶץ; וַיִּתְעַצֵּב, אֶל-לִבּוֹ. 6 And it repented the LORD that He had made man on the earth, and it grieved Him at His heart. מֶר יְהוָה, אֶמְחֶה אֶת-הָאָדָם אֲשֶׁר-בָּרָאתִי מֵעַל פְּנֵי הָאֲדָמָה, מֵאָדָם עַד-בְּהֵמָה, עַד-רֶמֶשׂ וְעַד-עוֹף הַשָּׁמָיִם: כִּי נִחַמְתִּי, כִּי עֲשִׂיתִם. 7 And the LORD said: 'I will blot out man whom I have created from the face of the earth; both man, and beast, and creeping thing, and fowl of the air; for it repenteth Me that I have made them.'
יג וַיֹּאמֶר אֱלֹהִים לְנֹחַ, קֵץ כָּל-בָּשָׂר בָּא לְפָנַי--כִּי-מָלְאָה הָאָרֶץ חָמָס, מִפְּנֵיהֶם; וְהִנְנִי מַשְׁחִיתָם, אֶת-הָאָרֶץ. 13 And God said unto Noah: 'The end of all flesh is come before Me; for the earth is filled with violence through them; and, behold, I will destroy them with the earth.
יז וַאֲנִי, הִנְנִי מֵבִיא אֶת-הַמַּבּוּל מַיִם עַל-הָאָרֶץ, לְשַׁחֵת כָּל-בָּשָׂר אֲשֶׁר-בּוֹ רוּחַ חַיִּים, מִתַּחַת הַשָּׁמָיִם: כֹּל אֲשֶׁר-בָּאָרֶץ, יִגְוָע. 17 And I, behold, I do bring the flood of waters upon the earth, to destroy all flesh, wherein is the breath of life, from under heaven; every thing that is in the earth shall perish.
יט וְהַמַּיִם, גָּבְרוּ מְאֹד מְאֹד--עַל-הָאָרֶץ; וַיְכֻסּוּ, כָּל-הֶהָרִים הַגְּבֹהִים, אֲשֶׁר-תַּחַת, כָּל-הַשָּׁמָיִם. 19 And the waters prevailed exceedingly upon the earth; and all the high mountains that were under the whole heaven were covered.
כג וַיִּמַח אֶת-כָּל-הַיְקוּם אֲשֶׁר עַל-פְּנֵי הָאֲדָמָה, מֵאָדָם עַד-בְּהֵמָה עַד-רֶמֶשׂ וְעַד-עוֹף הַשָּׁמַיִם, וַיִּמָּחוּ, מִן-הָאָרֶץ; וַיִּשָּׁאֶר אַךְ-נֹחַ וַאֲשֶׁר אִתּוֹ, בַּתֵּבָה. 23 And He blotted out every living substance which was upon the face of the ground, both man, and cattle, and creeping thing, and fowl of the heaven; and they were blotted out from the earth; and Noah only was left, and they that were with him in the ark. כד וַיִּגְבְּרוּ הַמַּיִם, עַל-הָאָרֶץ, חֲמִשִּׁים וּמְאַת, יוֹם. 24 And the waters prevailed upon the earth a hundred and fifty days. (Here, both HaAdamah and HaEretz are used.)
י וְאֵת כָּל-נֶפֶשׁ הַחַיָּה אֲשֶׁר אִתְּכֶם, בָּעוֹף בַּבְּהֵמָה וּבְכָל-חַיַּת הָאָרֶץ אִתְּכֶם; מִכֹּל יֹצְאֵי הַתֵּבָה, לְכֹל חַיַּת הָאָרֶץ. 10 and with every living creature that is with you, the fowl, the cattle, and every beast of the earth with you; of all that go out of the ark, even every beast of the earth. יא וַהֲקִמֹתִי אֶת-בְּרִיתִי אִתְּכֶם, וְלֹא-יִכָּרֵת כָּל-בָּשָׂר עוֹד מִמֵּי הַמַּבּוּל; וְלֹא-יִהְיֶה עוֹד מַבּוּל, לְשַׁחֵת הָאָרֶץ. 11 And I will establish My covenant with you; neither shall all flesh be cut off any more by the waters of the flood; neither shall there any more be a flood to destroy the earth.' יב וַיֹּאמֶר אֱלֹהִים, זֹאת אוֹת-הַבְּרִית אֲשֶׁר-אֲנִי נֹתֵן בֵּינִי וּבֵינֵיכֶם, וּבֵין כָּל-נֶפֶשׁ חַיָּה, אֲשֶׁר אִתְּכֶם--לְדֹרֹת, עוֹלָם. 12 And God said: 'This is the token of the covenant which I make between Me and you and every living creature that is with you, for perpetual generations: יג אֶת-קַשְׁתִּי, נָתַתִּי בֶּעָנָן; וְהָיְתָה לְאוֹת בְּרִית, בֵּינִי וּבֵין הָאָרֶץ. 13 I have set My bow in the cloud, and it shall be for a token of a covenant between Me and the earth. יד וְהָיָה, בְּעַנְנִי עָנָן עַל-הָאָרֶץ, וְנִרְאֲתָה הַקֶּשֶׁת, בֶּעָנָן. 14 And it shall come to pass, when I bring clouds over the earth, and the bow is seen in the cloud, טו וְזָכַרְתִּי אֶת-בְּרִיתִי, אֲשֶׁר בֵּינִי וּבֵינֵיכֶם, וּבֵין כָּל-נֶפֶשׁ חַיָּה, בְּכָל-בָּשָׂר; וְלֹא-יִהְיֶה עוֹד הַמַּיִם לְמַבּוּל, לְשַׁחֵת כָּל-בָּשָׂר. 15 that I will remember My covenant, which is between Me and you and every living creature of all flesh; and the waters shall no more become a flood to destroy all flesh. טז וְהָיְתָה הַקֶּשֶׁת, בֶּעָנָן; וּרְאִיתִיהָ, לִזְכֹּר בְּרִית עוֹלָם, בֵּין אֱלֹהִים, וּבֵין כָּל-נֶפֶשׁ חַיָּה בְּכָל-בָּשָׂר אֲשֶׁר עַל-הָאָרֶץ. 16 And the bow shall be in the cloud; and I will look upon it, that I may remember the everlasting covenant between God and every living creature of all flesh that is upon the earth.' יז וַיֹּאמֶר אֱלֹהִים, אֶל-נֹחַ: זֹאת אוֹת-הַבְּרִית, אֲשֶׁר הֲקִמֹתִי, בֵּינִי, וּבֵין כָּל-בָּשָׂר אֲשֶׁר עַל-הָאָרֶץ. {פ} 17 And God said unto Noah: 'This is the token of the covenant which I have established between Me and all flesh that is upon the earth.'
It seems clear from the above that the Torah text is emphatic in saying that all animals on earth and all humans on earth perished, who were not inside the Ark.
It is true that the Talmud sages had a disagreement regarding whether the Mabul Mayim disturbed the bones in the land of Israel, but in that discussion all participants acknowledged that everyone outside the ark died. They even discuss why Og and the Reim (giant sea creature) didn't die, and conclude that they survived by being physically attached to the ark. The rabbis of the Talmud additionally opine that animals were killed because they engaged in unnatural sexual acts, but the fish did not.
So it seems to me that the Talmud does not dispute in the least that everyone outside the ark died. That is to say, there is no tradition that seems to suggest Genesis 6-11 were not literal, and that people were left alive outside the ark.
According to Jewish Tradition, the Flood happened in the Traditional Hebrew Year 1656, which corresponds (within some error margin) to the year 2104 BC. Ussher's chronology, based not on Hebrew Tradition but based on a literal reading of Genesis finds the flood having occurred at 2348 BC.
However, the above situation does not seem to fit at all with what we find in science, history, and archaeology. For an overview of the problems, you can see this: http://www.talkorigins.org/faqs/faq-noahs-ark.html
Here is a list of major problems:
Archaeology and history. The Egyptian Old Kingdom seems to transition smoothly into the Egyptian Middle Kingdom, as we can see from language, economy, knowhow, etc. The Pyramid of Cheops, the Pyramid of Djoser, etc. were built prior to 2500BC, whereas Senusret II and III pyramids were built after 1900BC. It seems obvious from the Egyptians were not wiped out by the flood. The closest hint I can even find is a tiny erosion in the sphinx: http://en.wikipedia.org/wiki/Sphinx_water_erosion_hypothesis
Genetics. Regardless of when the flood happened in the last 10,000 years, we would have a genetic bottleneck in all humans and animals. Humans for example would all come from one father who lived in the last 10,000 years. This is testable, but in fact no bottleneck is found. The closest bottleneck I can find is the Toba catastrophe theory that says humans may have been reduced to 10k individuals 70,000 years ago: http://en.wikipedia.org/wiki/Population_bottleneck#Humans
Long lived plants were not killed by this flood. The Pando clonal colony have been around for an estimated 80,000 years: http://en.wikipedia.org/wiki/List_of_longest-living_organisms#Clonal_plant_colonies
Geology and Genetics: Geologists would conclude that Australia separated from Pangaea over 100M years ago. The Kengaroos, Koalas and other marsupials that live there should have genomes that diverged around that time (To be fair, I know little about genome sequencing of marsupials but there seems to be a major discrepancy because molecular genome estimates say Marsupials diverged no earlier than 60 million years ago: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000436 whereas other sources conveniently claim 160M years ago http://www.nature.com/nature/journal/v476/n7361/full/nature10291.html%3FWT.ec_id%3DNATURE-20110825). In any case, genetic drift of isolated populations on different continents should show up as divergence in the genomes with their cousins on other continents. This would show evolution over millions of years, not 4100. Does anyone have any examples? Admittedly I am not expert in this and have a hard time finding it.
Geology, Paleontology and Physics: The Geological Principle of Superposition, the fossil record (index fossils) and the radiometric methods can all be calibrated to agree with one another. This one contradicts "flood geology" by Creationist scientists which claims that the sediments were laid down by the flood. TalkOrigins puts it very well:
Creationists, on the other hand, must explain to us how sediment and rock laid down in a mere year can yield such fantastic, orderly differences in radiometric ages. This poses a fatal problem whether one believes in the accuracy of radiometric dating or not! One would think that the flood sediments (gathered from the four corners of the old antediluvian world) and their associated igneous rock (formed during the flood) would all register very little radiometric age. At the very least we would expect random fluctuations if the radiometric methods were totally at sea. Why should the percentage of lead to uranium in zircon crystals (the key to ordinary uranium-lead, radiometric dating) depend on which geologic period they are found in? If most of the geologic column were created during Noah's flood, would it really matter whether a zircon crystal was found in Cambrian strata or Cretaceous strata, in Jurassic strata or Tertiary strata? Noah's flood might just as easily deposit the same crystal in one place as another. http://www.talkorigins.org/faqs/hovind/howgood-gc.html
In short, the flood had to be universal (even if local) because of Jewish theological considerations, and a universal flood contradicts a lot of known history, biology, geology etc.
The main problem is that these sciences are independently able to arrive at a consistent picture of the world. Perhaps one or two techniques by themselves would be wrong. Perhaps they could be off when extrapolating into the millions of years. But we are talking about ALL of them being wrong, and about the last 10,000 years. How to reconcile the two views?
Finally, here is my biggest worry. Doesn't Bayes' Theorem in that case disprove Judaism:
P(A) = P(B) * P(A given B) / P(B given A)
If A is Judaism and B is the universal flood, we have:
P(A given B) = I'll be generous and say 99%, meaning Christianity, Islam etc get 1% combined
P(B given A) = Theological considerations above would suggest 90%,
but I will be generous and say Judaism only 20% insists on a universal flood
P(B) = Probability of a universal flood is super super low, like 0.1%
Multiplying seems to disprove Judaism to me. That combined with all the other stories like the exodus of 3 million Jews etc.
So how do I reconcile the two worldviews?