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In this country a criminal defendant does not have to prove himself innocent. He is already presumed innocent unless or until the state can prove him guilty beyond a reasonable doubt. There are many ways that a good trial lawyer can create doubt in the minds of a jury, through cross examining the state's witness and, if he chooses putting on a defense of his own. And if he's successful at establishing reasonable doubt as to the facts of what happened, then his client has to be acquitted.
There are also defenses to rape that can be relevant and useful to the case, depending on the facts and circumstances. You mentioned that the defendant has an alibi, which if it's strong enough, can lead to an acquittal. Consent can sometimes also be a defense to a rape case, if the facts tend to bear that out. A dishonest complainant with an axe to grind can be a potential defense. Mistaken identity may be a possible defense or, as you indicated, a lack of evidence, or some combination of these and others.
So again, a defendant never has to prove anything. All proof is left to the state and if they can't show it beyond a reasonable doubt they lose. It's the lawyer's job to work with the facts he or she has to establish that doubt.
Thank you for the additional information. Defense strategy always depends on the facts and circumstances of the state's case: what is in the police reports, what the forensic evidence shows, what the witnesses will testify to.
You need an experienced criminal lawyer. If you have witnesses who can place you elsewhere at the time of the alleged rape, you need to give your lawyer the names and contact information for those witnesses so that he can interview them. You can ask him for copies of the police reports and discovery material and look them over. Tell your lawyer anything you see that you think is incorrect. If he asks you any questions about what he sees on the reports, answer him truthfully. No lawyer likes to be surprised in the middle of a trial by facts his client knew about but never told him.
A good attorney client relationship involves trust and communication. If you don't have that, you've got the wrong lawyer.