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Prue goes through a lot in the first half of Season 3. One of the major plot lines for her is her relationship with Wyatt, and her trying to repair their relationship and pick up the pieces of what happened with the Shadow Witches.

In Like a Phoenix, I Rise, The Elders have refused to bless Chris and Bianca's wedding, which really upsets Chris who asks Prue for her help. She then goes to see Alyssa and gets Alyssa to agree to bless the union - after a few failed threats, but Alyssa states that she's only doing it to stay in good relations with the Halliwell Family. Prue is later seen helping Bianca prepare for her wedding to Prue's brother-in-law and cousin. The two seem happy and in a good place. Prue also gives Bianca the headband that she wore on her wedding day but states that she has to give it back. Unbeknownst to Prue, the Shadows are planning to ruin Bianca's wedding and pit the Halliwell's against Bianca.

A few minutes before the wedding starts, Tamora arrives with her hair a mess, and Prue can't resist setting her sister-in-law straight and tell her the hard truth. She tells her to grow up, forgive herself, and move on from Mike. Tam refuses to admit her demon-hunting problem has to do with Mike, but Prue doesn't believe her. Charlotte tries to stop Prue, but Prue tells her to stop and that Tamora needs to hear it. She tells her the cold truth before telling Tam to get ready for Chris' wedding and leaves.

At the wedding, Prue, who is a bridesmaid, is talking to Eric when Charlotte walks over and they stop. Charlotte is a little bothered by it and confronts her sister about it, and Prue tells Charlotte her side of the story and then excuses herself. During the wedding, Prue wears a green dress and walks down the aisle ahead of Bianca and with the other Bridesmaids. When a manipulated Bianca steals Alyssa and then Chris' powers Prue is among the few people to think the best out of Bianca. As she struggles to sort things out, she realizes that Siobhan is behind the attack and tries to solve the problem and save Bianca.

Wyatt shows up at the attic and Prue tells him he isn't welcome there, and he leaves. In their bedroom and Prue is mad - really mad. Wyatt tries to settle her down but it's no use. They have a bad argument. By the end of the episode, the Destined Ones have solved the problem of Bianca and rescued her. Bianca and Prue are in a good spot. Wyatt and Prue, are not and have a lot to work out.
In Evil Becomes Her, Prue is faced with the wrath of an evil Charlotte who is blinded by her own magnified anger. Charlotte and Prue have a bad fight and Charlie says a lot of bad things that hurts Prue. When Charlotte's anger is released she is mortified by what she said and Prue needs some time to deal with the things her sister said. Prue deals with other obstacles throughout the obstacles including her marriage to Wyatt being strained and tells Charlotte why she and Eric have been close lately. Prue also exchanges words with a new customer named Conrad.
In My Inner Whitelighter, Prue and Charlotte are still not on good terms despite Melinda's hardest attempts to make things good between them. Prue always mentions that she misses the powers she had as a Shadow and sometimes longs for them despite knowing they are wrong. Prue and Conrad, a customer who keeps showing up at P3, grow a little closer.
In Whatever You Do, Don't. Turn. Dark!, Prue and Chris spend time together and confide some secrets to one another. Prue also interacts with a baby, which prompts Prue and Wyatt, who find themselves in a better spot, to talk about having children in the future and they agree to practice. Conrad appears again with Prue and makes a move, although Prue declines.
In As Dark as Jarves, Wyatt prepares a special surprise date for Prue. Prue declines Conrad's attempts to kiss her again, which angers Conrad. He then kidnaps her and is revealed to be a demon. Her family figures out she was kidnapped and by who and try to save her. As Conrad confesses his story to Prue, she is shocked to learn his true identity is Conrad Turner and he is the younger half-brother to Cole Turner. She manages to get him to change his mind about killing her and senses that he isn't a bad person, and learns that his love for her as managed to save him from evil. When Wyatt shows up to save her, he tries to vanquish Conrad but Prue stops him and lets Conrad get away. Wyatt is astonished and hurt and leaves. Prue and Wyatt have a bad argument about Conrad and Wyatt leaves making Prue devastated.
Prue turns evil in Halloweentown and does some things she wouldn't do otherwise.
In Legacy of the Father, Prue's powers allow her to confirm Melissa's story about Elliot is true when she touches Melissa. Her powers also tell her that the Medallion is not good, and she tells Wyatt to destroy it and leave whatever they have uncovered alone. Wyatt doesn't. She also tells Melinda that she's been having strange dreams that are really bothering her, and Melinda kind of brushes it off as stress at first. Prue also summons Raina to help with the Medallion and the feeling she got and starts to think about marriage counseling.
Throughout What Hurts the Most and Lost Girls, Prue is struggling a bit to find answers for everything that is going on. She feels a little bombarded by the information but takes it in pieces. She also comforts a grieving Tamora over Sebastian's death, is seeing a marriage counselor with Wyatt, and still having nightmares about The Darkness. She also is given The Book of The Angels to look after.

In From This Forgotten Prison, Prue's dreams about the Darkness take center stage and she is determined to figure them out. She reads the BOAngels and finds out a lot of interesting things, but is struggling to read it because of the language it is written in. When she confronts Wyatt about what has been going on with him lately and about what Chris said to her about him, Wyatt lies to her about hunting Conrad and tells her not to worry about it. Naturally, this makes Prue dig her heels in even more. Melissa and Prue share a strange scene in which Melissa thanks Prue for her help when Prue visits Wyatt at the Bay Mirror. The two girls seem to be getting along better.

Prue and Wyatt are tricked by a glamoured Ignatius into giving blood to him for "blood testing day", as Ignatius needs their blood to release the Darkness. Prue is referenced throughout the episode as, "Tsunami Prue" by Melinda, Damon, and once by Wyatt when they are talking about what Prue will do when she finds out Wyatt has been hunting Conrad. Everything is pushed to the back burner when Prue starts to feel that the Darkness is being released.
In Stand by You,
In Darkness is Here,

In Tell me what's your Fear, I'll tell you how you'll Die, Wyatt and Prue are having a very romantic dinner together when a fight breaks out at the restaurant. Prue convinces a reluctant Wyatt to freeze the entire restaurant before they call the cops. Junior tells them that they did the right thing calling the police and that things have been really weird with people lately. Wyatt gives Prue his car keys and tells her that he'll orb home after doing some demon hunting.