Dr. Joe Werner, Ed Bauer's best friend from medical school, arrived at Cedar's Hospital in 1966. Although he was several years older, Joe had been Ed's closest friend in medical school. Joe came from a less privileged background than Ed and had struggled longer to get where he was. Now a resident at Cedars, Joe was envious that the eminent Dr. Jackson was bestowing so many professional favors on Ed, and that the way was already paved for Ed to become the chief surgeon's son-in-law. Not one to be passed over, Joe vowed to get a piece of Ed's action any way he could. Joe's opportunity seemed to arise when Ed broke up with Leslie Jackson, because he was concerned that marriage would hurt his illustrious surgical career, Convinced that marriage would not serve his illustrious surgical career, Joe quickly moved in. Before long, Leslie accepted Joe's proposal of marriage. At this point, Steve Jackson suffered a coronary. During Steve's absence, Joe used his chief resident position at the hospital to saddle Ed with menial duties. The enmity between Ed and Joe reached a climax when Joe started dating the voluptuous Tracy Delmar. Tracy introduced herself to Sara McIntyre as her long-lost niece and ingratiated herself with the lonely lady doctor. She was immediately attracted to the coolly ambitious Joe and charmed him into going out on a date one night, when he was supposed to be on duty. While they wined and dined, one of Joe's patients died. Joe seized the opportunity to pin the blame on Ed, who had forgotten to sign out earlier that afternoon when Joe relieved him. Joe would later prove that he did have a conscience after all. Joe was awed when Ed saved the life of Marty Dillman, the leader of a neighborhood gang known as the Lords, Marty had been stabbed during a rumble and would have died had it not been for Ed's brilliant surgery. As a result, Joe wasted no time in dumping the shallow Tracy and apologizing to Ed, acknowledging him as the fine surgeon that he was. The doctors decided to let bygones be bygones and soon became inseparable friends with Joe gallantly stepping aside to let Ed pursue Leslie.

Not long after, Joe fell in love with Sara McIntyre. Though he tried to break through her icy exterior, the fear of commitment drove Sara to push him away. Then Joe was offered a chance to go on sabbatical overseas. Elated at the chance, he asked Sara to accompany him, but unfortunately, she refused. When Joe returned to Springfield months later, he was shocked to learn that Sara had impulsively married her patient, Lee Gantry! Suspicious, he did some investigating and warned Sara that Lee was a dangerous man who was only after her money. It turned out he was right. When Lee (who'd been gas lighting Sara) saw her looking at his late wife's diary, he suddenly attacked her. Luckily Joe saved her, while Lee fell to his death. The harrowing ordeal over, Sara married Joe. Though the pair deeply loved each other, their marriage came under strain due to their long work hours and Sara's guilt over not being able to give Joe a child. No longer communicating, Joe fell prey to the charms of Charlotte Waring and the two started having an affair. Though he tried to keep the affair secret, an anonymous person sent Sara a letter telling her that her husband was having an affair. Confronted by Sara, Joe confessed and insisted the affair was loveless. Then tragedy struck: Charlotte was rushed to the hospital after apparently suffering a heart attack. Though he tried to save her, his efforts failed and Charlotte died.

In the wake of John Fletcher's disappearance and Charlotte's untimely death, Joe required Ed to work extended hours at Cedars. Joe was in deep trouble due to his bungling of Charlotte's case, and although Ed tried desperately to salvage his friend's career, Bruce Banning pushed hard for Joe's demotion. Hard-nosed osteopath Dr. Wilson Frost went so far as to insist that Joe be dismissed from the staff. Unbeknownst to Joe, Wilson had feelings for Sara. Under pressure from the medical review board, Joe resigned from Cedars and Ed became a reluctant chief of staff. Ed felt double guilty when Adam Thorpe came to Cedars as an independent contractor to analyze the hospital's efficiency and recommended that Ed remain in Joe's former position. Depressed, Joe left Sara and starting drinking heavily. Despite Ed's attempt to turn him around, Joe took to drink and holed up in a cabin with the unstable KitVested (who had murdered Charlotte since Charlotte double-crossed her by sending Sara the anonymous note) as his only link to the outside world. Kit didn't waste any time in telling Joe that Wilson Frost was pursuing Sara, but she left out the part about Sara not reciprocating Wilson's feelings. Kit decided to have Joe to herself by keeping him isolated from his friends and encouraged his drinking in the hopes that he'd stay with her forever. Eventually Kit completely lost her mind. She made a phone call to Sara and tricked her out to the cabin and then Kit poisoned Sara. Kit then shot Joe, only to be fatally wounded while struggling with Joe over the gun! In the end, Kit was dead and the Werners resumed their marriage.

Their marriage stronger than ever, in 1975, the couple decided to adopted a little boy named Timmy. Unfortunately soon after, a man named Spence Jeffers started sending notes to Sara and Joe stating that Timmy, or "T.J" as he was called, had been adopted illegally and was really his son. Sara and Joe were livid and it didn't help any when Joe had to go to India for job reasons. Sara asked her good friend Mike Bauer to investigate Spence's claims and Mike eventually disproved the validity of Spence's claims about T.J. Unfortunately, before Mike could show how wrong Spence's assertions were about T.J., Joe would have a massive heart attack while in India and died. Sara always suspected that the stress put on Joe because of Spence's claims was what caused Joe's fatal heart attack.