"Ulysses" begins with Xena and Gabrielle wandering along the shoreline of a beautiful beach. While Gabrielle muses about life and the beauty of nature, Xena is distracted by a battle occurring on the beach. They watch a skillful lone fighter is battling a group of pirates. Xena admires his fighting style until the addition of more pirates makes it an unfair fight, and Xena and Gabrielle join in to help him defeat the pirates.
Following the fight, Ulysses introduces himself to the women. Although his name means nothing to Xena, Gabrielle immediately recognizes him as the rightful King of Ithaca. Ulysses explains how Poseidon, God of the Sea, is preventing him from returning to his country. With an immediate attraction to Ulysses spurring her on, Xena volunteers her and Gabrielle's services to Ulysses to assist him in returning to his homeland.
Further along the shoreline, the trio are confronted by Poseidon, God of the Sea, who warns Xena against providing any kind of help to Ulysses. Poseidon seems to hold a grudge against Ulysses because he blinded Poseidon's Cyclops Polyphemusand he warns Ulysses that there is nothing left on Ithaca now that his wife, Penelope, is dead. After Poseidon's departure, Ulysses explains to the women how he had heard from fishermen that his wife had perished in a storm at sea after setting out to find him.
Traveling back onto dry land to formulate a plan, Xena warns Ulysses that during the battle of Troy, where Ulysses had been fighting for ten years, that she had fought on the opposite side against the Greeks. Ulysses assures her that this does not matter, and that his only quarrel now is with those preventing him from returning to Ithaca.
Later that night Ulysses scouts out his ship, which has been taken over by pirates. While Gabrielle sleeps, Xena and Ulysses share a cosy moment by the fire, getting to know each other better. The attraction between the pair is obvious as they discuss their plans for taking back his ship.
Early next morning, the trio sail out to take over Ulysses ship. Gabrielle acts as a distraction, gaining access onto the ship by disguising herself as a dancing girl. While the pirates are distracted, Ulysses and Xena get on board and, catching them by surprise, fight all the pirates and throw them into the sea. However, Ulysses suffers an injury when he attempts to shield Gabrielle from an arrow shot by the last remaining pirate. Not knowing that Xena could have stopped it, he takes the arrow in his shoulder, which requires Xena's skills in doctoring to remove it.
Below deck, Xena attends to Ulysses' wound, and he remarks upon Xena's gentle touch. The pair discuss their own unique weapons: Xena's chakram, and Ulysses bow, which he only can string, and which remains on Ithaca. The pair share a moment where they almost kiss, before being interrupted by a very unwell Gabrielle, who is suffering badly already from seasickness.
Xena and Ulysses discuss the best way to return to Ithaca. The most direct route involves taking the ship past the Island of the Sirens, who use their song to call all men to throw themselves upon the rocks and perish. Xena assures him that she is more than capable of getting them past the island safely.
As the trio journey towards Ithaca, Poseidon sends some dreadful storms and weather to try and slow their boat down. Poseidon's obstacles prove unsuccessful in slowing them down, and their biggest challenge appears in the Island of the Sirens. For Ulysses own safety, as they come close to the island she ties him to a post, so that he does not endanger them all by taking over the ship in response to the Siren's song.
As they near the island, the Siren's Song immediately takes its hold on Ulysses. A very seasick Gabrielle is below deck with Ulysses when he loses his mind, and in his mad hurry to get to the Sirens, he attacks Gabrielle. On deck Ulysses fights Xena to get control of the wheel of the ship. When that fails, he attempts to get off-board to swim to the island. Sensing the significant danger they are in, Xena starts to sing, using her beautiful voice to drown out the sounds of the siren song. Finally, they pass the island completely, and Ulysses is returned to his normal state. Overcome with gratitude to Xena, Ulysses thanks her profusely, and is horrified when Gabrielle comes limping on deck from the injury he inflicted while under the Siren's spell.
Below deck later that night, Xena brings Ulysses some food. While Gabrielle sleeps, Ulysses declares to Xena that he is falling in love with her, and invites her to stay with him on Ithaca when they arrive. He explains that though he loved his wife, he is ready to move on and start a new life, and he believes that in Xena he has found his soul mate. They share a passionate kiss, and Xena tells Ulysses that she will think about his offer. Unbeknownst to them both, Gabrielle had lain awake listening to the whole exchange.
The next day Ithaca comes into view. As an ecstatic Ulysses celebrates, Xena and Gabrielle have a quiet discussion about what Gabrielle overheard the night before. Xena is overcome by her feelings for Ulysses, and thanks Gabrielle for all she has taught her. Without Gabrielle, Xena says, she could never love Ulysses the way she does. Both Xena and Gabrielle are shocked to hear Xena use that word, but Xena acknowledges that is how she is feeling about Ulysses.
The trio steer the boat on-shore, and Ulysses celebrates his return to Ithaca. As they journey further into the island they come across a lone man being attacked by a number of pirates. The group intervenes, rescuing the man, who then recognizes Ulysses as his childhood friend. Overjoyed to see his friend, Ulysses' excitement is dampened when his friend mentions how thrilled Penelope will be to see him. It turns out that Poseidon had created the lie about Penelope's death so as to deter him from returning to Ithaca, which Poseidon had promised to his pirates as a reward. At that very moment, Penelope was choosing a suitor to make the new King of Ithaca.
While they make their way to the castle, Xena comes up with a plan of how to deter Ulysses' attention from her, knowing that his rightful place is beside his wife as King of Ithaca. At the castle they gain access through a secret passage Ulysses used as a child. Under the castle, Xena and Ulysses enter a heated argument, where Xena denies having feelings for him at all, implying that it was all in his head. Ulysses is clearly distressed, but chooses not to believe Xena. Putting it out of their minds, they put on disguises and enter the grand hall where a competition is under way.
Penelope has made the challenge for all potential suitors to string Ulysses' bow. It is well known that only Ulysses can string the bow, so Penelope agrees to marry whoever can string it. As the numerous pirates fail, a disguised Ulysses asks for a chance. He takes his place at the bow, but the years have had their effect, and he is unable to string it. Realizing what is at stake, Xena sneaks under the table, and helps Ulysses to string the bow, at which point he reveals himself to all as the Ulysses, the rightful King of Ithaca, returned to take back his throne.
As Xena and Gabrielle prepare a boat to leave, Ulysses makes one last offer to Xena, begging her to allow him to go with her, so that they may be together. He has realised what Xena was trying to do earlier, and tells her that it only makes him love her more. Despite this, Xena is firm in her decision for Gabrielle and her to leave alone. She sends him back to his wife so that he may continue his destiny on Ithaca, and Gabrielle and Xena can continue their journey together.