Hawes is first seen during a period where Holmes has no active cases. Bored, he takes Watson to the morgue in the Medical Examiner building. Holmes and Hawes have an agreement in which they play chess with the stakes being Holmes having access to the corpses and Hawes playing for money. Holmes wins the game and discovers a case while examining a corpse. ("Ancient History") Hawes performs the autopsy on Haley Tyler and confirms to Watson that though Haley fell from a balcony, her abdominal aorta was first severed by someone who knew exactly where to stab her. ("Blood Is Thicker")
Hawes delivers sad news to Detective Bell that an idol of his, Manny Rose, shot and killed a murderous street thug in order to protect a young woman. Rose was then killed by companions of the thug. ("The Hound of the Cancer Cells") Holmes takes on a case for MI6 which involves investigating the murder of Arthur West. He and Watson are shown into the morgue by Dr. Hawes and discover that the arms from West's corpse are missing which shocks Hawes as they were present when the autopsy was performed. Hawes is sporting a beard. ("Art in the Blood")
Hawes reports the results of an autopsy on Melissa Ledbetter, a nurse that Watson knew from her time as a doctor. He mentions that Melissa was beaten in the head many times before being strangled and that she had someone else's DNA under her fingernails. Later, how shows that another victim had severe brain damage that was very quickly and recently obtained. ("The Eternity Injection") Hawes tries to tell Holmes and Watson how a frozen woman died but they are able to deduce she was hit in the head before being exposed to refrigerant by examining the body. Holmes tells Hawes not to sulk and he tells them which refrigerant was used which gives them a suspect pool. ("T-Bone and the Iceman")
Hawes reviews the autopsy of Garrison Boyd with Holmes. Boyd was a professional "debunker" whose skull was caved in and had a tip of a garden gnome's hat lodged under his eye. ("A Stitch in Time") Hawes next deals with several murder victims who have had internal organs removed in order to make room for transporting drugs. Watson is able to identify the doctor who made the stitching in the bodies. ("Under My Skin")
Hawes helps Tim Wagner's father identify his son's body. ("Tag, You're Me") Hawes participates in the analysis of the burnt body of Eddie Ross. ("The Games Underfoot") Hawes provides Holmes and Watson with the autopsy of Ellen Jacobs who died from suffocation, inhaled sodium thiosulfate and was eight weeks pregnant. ("A Burden of Blood") After helping ME officer Nicole Slater put a body in storage, Eugene asks her out to a NY Ranger game and she accepts. Excited, they both start to sing "Coal Miners Daughter" when an explosion kills Slater and injuries Hawes. He deduces that a bomb was placed in the body in order to erase evidence on Honduran gang members stored in the morgue. ("Down Where the Dead Delight")
Hawes allows Sherlock to examine a body that fell many stories and killed another. ("Up to Heaven and Down to Hell") Holmes meets Hawes in the morgue to inform him that Hawes contaminated a DNA sample with his own, complicating a case. Sherlock plays chess with Eugene and expressed his concern, pointing out that he's beating him easily but Eugene says he's fine. Later in the hallway, Sherlock makes a plea to Hawes and reveals his past situation with Jamie Moriarty and tells Hawes he's not well and won't see him go down the same dark path he did. Hawes admits he's hurting. Eugene shows up at The Brownstone, tells Holmes he's taking time off and may change jobs. He gives Holmes a list of MEs for him to pick from to work with while he's gone. ("Hounded")
Watson goes to see Hawes perform at a stand-up comedy club. After some initial heckling, Hawes does fine and Watson is relieved and happy for him. Hawes mentions to Watson the stand-up is part of his therapy, that he's doing better and will be back at work soon. Watson says that Sherlock couldn't come because it's his girlfriend's birthday. Hawes is surprised that Sherlock has a girlfriend and wants to hear more but Watson is called away. ("Ain't Nothing Like the Real Thing")
Hawes returns to work and provides Gregson, Holmes and Watson with confirmation that a chef was killed with snake poison and that it will take time to identify from what kind of snake. ("Ill Tidings") Hawes suspects foul play when he finds the stomach contents of a victim contains horse tranquilizer and human remains. Holmes inhales the bag of stomach contents which disgusts Hawes. ("How the Sausage Is Made") Sporting a moustache, Hawes examines the remains of two victims that were burnt in an incinerator, one alive when burnt. He identifies a piece of metal as an orthopedic foot brace worn by one of the victims. ("High Heat")
Hawes hobbles into the morgue on crutches, having torn his achilles tendon playing softball and finds Holmes laying on an autopsy table. He jokes with Holmes and tries to find out why he's waiting for test results in the morgue instead of at home. ("An Infinite Capacity for Taking Pains")
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A lot of these stand-ups at these open mics talk about bombing, but, hey, I've lived through a real bombing.