It all makes sense now—well, most of it anyway. Amy seduced Desi so there would be evidential bodily fluids that could allow her to accuse him of rape; her whole body also bears injuries consistent with forced sex. During the medical examination, Boney holds Amy's hand and Amy actually catches her smiling, like she's glad Nick didn't do it.
Police are already on the scene at Desi's house, where Amy pretty much butchered him in his sleeping pill stupor. Her story will be that she slit his throat, then used the knife to cut herself free and left the house in his car, thinking about nothing except escaping. So far, people are buying it—even the doctor continues to believe her pregnancy story and says that she miscarried.
Back at the police station after she's released from the hospital, Amy is reunited with her parents, who are obviously beside themselves and probably secretly enjoying the publicity as reporters outside snap photos. Amy is then taken to an office for a conference with the police where she tells her story to Boney.
Here it is: Amy claims that Desi has always been quietly obsessed with her, but her and Nick's move back to the Midwest, placing her in such close proximity to him, pushed him over the edge. When he arrived, he barged into the house and there was a struggle that led into the kitchen, where he stabbed her in the arm. Conveniently, Amy's able to show Boney the scar (that she gave herself). She then was knocked out and woke up tied up in the living room. Desi was in the kitchen straightening up things that fell over, then decided at the last minute to make the living room scene look worse by knocking over the books and overturning the ottoman.
While Amy completely implicates Desi in her disappearance, she doesn't do much to make Nick look any better—she still claims that the rape and anger fits in the diary are true and that Nick really did hide his credit card purchases in the woodshed. She also claims to be unaware of the sinister backstory to Punch and Judy, saying she found the puppet family online and thought it would be a perfect gift for the fifth-anniversary wood theme.
But back to Desi. According to Amy's story, he threw her in the trunk of his car and drove to Hannibal, where he ditched her purse. Boney immediately says that there are a lot of odd coincidences in the case, like Desi stopping in Hannibal, the same place Nick's anniversary clue led him. Amy, though, turns all this back on Boney and accuses the cops of botching her case. Obviously, we know the truth—but Amy seems to have covered all her loose ends. It's impressive, and impressively creepy too.