What flaws does Odysseus show in Book IX of Homer's The Odyssey? 

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In terms of his flaws, Odysseus shows some greediness in this book.  Prior to the Cyclops' return to his home, Odysseus's men try to convince him to take some food and return to their ship; however, he "refused -- far better had [he] yielded."  He hoped that the owner of the cave would return and "offer gifts," a custom in Greece at the time because travelers were protected by Zeus.  If a host could manage, he would often provide a traveler with a guest-gift, meant to honor the guest; however, a guest was never supposed to take advantage of his host, and Odysseus is pretty presumptuous in his assumption that such a gift would be offered.  It would have been better to be safe and return to the ship with only what they needed rather than tempt fate and risk the life of his men, some of whom he does lose to the Cyclops as a result.

Further, Odysseus's pride makes a big appearance as he and his men row away to escape the angry Polyphemus.  He taunts the monster, shouting back that Zeus has punished him for his actions and that he got what he deserved when Odysseus and his men blinded him in his cave.  Polyphemus then tears off a hilltop and throws it at them, and when it lands in the water ahead of them, it pushes them back toward shore!  Despite this danger, after they've rowed away again, Odysseus ignores his men's pleading and shouts once more.  He tells the Cyclops, "if ever mortal man asks you the story of the ugly blinding of your eye, say that Odysseus made you blind [...]."  This was such a stupid move because now the Cyclops knows his name and can pray to his powerful father, Poseidon, god of the sea, to seek revenge on Odysseus.  His pride, and wanting to be given credit for the besting of the Cyclops, prompted Odysseus to give away the information that will allow him to be identified.  Seeing as how Odysseus must travel by sea to get home, his pride materially damaged his chances of getting home quickly and safely.