Reporter: Before the DNA test come back on Michael Jones, detective Alan Foote gets an unexpected visit from inn budnytska. She came to my office and said, she didn't know if she was dreaming or if it... See More
Reporter: Before the DNA test come back on Michael Jones, detective Alan Foote gets an unexpected visit from inn budnytska. She came to my office and said, she didn't know if she was dreaming or if it was a reality, but she remembers being in the hotel room and sitting on the bed and across from her was a black male. Reporter: Wow. Wow is right. Reporter: Detective foot shows inn a photo lineup, including a photo of Jones. And he asks me if I recognize anybody. And I chose a person from the lineup. This is the person who basically -- who raped me. Reporter: It's all starting to come together. And then the DNA results finally arrive. So you got the DNA results. What did you think at that moment? I called ken up and I said, you're not going to believe this. Detective Foote calls me up, he says, hey, ken, you're not going to believe this. He goes, it's him. I go, no, yeah, no kidding. Reporter: What was that moment like? Oh, it was total elation, you know. I was happy. Reporter: It's enough for an arrest warrant and a trip back to Maryland to see Michael Jones. Now, it's time to make an arrest. Right. Reporter: How does that happen? I fly to Frederick, Maryland. I meet up with ken Brennan and members of the Frederick police department. I fill them in, that I have got the warrant. So, we all head out. We're caravanning like John Wayne and the wagon train where the cavalry is coming because we're going to go get our guy and we go to his apartment -- and there he is. We knock on the door and he comes to the door and he answers. And we look at each other face to face, and I said, "I told you I'd be back." You are being charged with rape, all right? She says I raped her? We already have the hit on the DNA. Okay? Now, it's just a question of interrogating him and seeing if I can get this guy to roll on it. Reporter: In this interrogation room, Foote and Brennan begin a good cop/bad cop routine. Look at these. . I didn't do that. You were there. I did not do that. You were there. Reporter: And Jones tries to explain away the DNA match. Once we started to throw the fact that, obviously, he was under arrest for this kidnapping and rape, his story changed. Give us your version of what went down. And you only get one chance at it. All right, I'm going to be straight up. I know the only thing he's going to come up with is, "She was a prostitute. I paid for her. She was fine when I left her. I have no idea what happened to her after." Because they already have their cover story, okay? Reporter: Sure enough, Jones claims he went out with his friend in the Mercury t-shirt to a strip club that night. As he returned to the hotel, he says he saw inn hanging out front with some other women. Obviously, they were hookers or whatever. And you know, we were talking to her like, you know, "What to have some fun?" Okay? And then what happens next? Did you go to her room? Did she go to your room? We went to her room. You went to her room? Uh-huh. And then, you know, she -- she whispers in my ear, "A hundred bucks." So we did it and I gave her a hundred bucks and I left. Easy victim. Easy victim for everybody. Easy to blame you. Easy to blame. And then what happened after that? After you had sex with her? I went back to my room. So, you don't know what happened to her? That's what you are telling me, right? Yes sir. Reporter: Unfortunately for Jones, the hotel cameras tell a different story. It's true that he and his friend were talking to some women at 3:33 when inn left to get that phone card. But look. She walks right by without ever talking to anybody. There wasn't any kind of an exchange between the two of them that would have been indicative at all of somebody slis soliciting a prostitute or a prostitute soliciting a John. Reporter: And then there's this. The hotel records show that Jones didn't check out of his room until February 22nd, one full day after the attack. So, why would he be seen leaving with his suitcase at 5:28 the morning before, only to return without it an hour later? So he put his suitcase in the trunk of the car. But he never came back to get the suitcase. Whooid you leave the hotel when you weren't supposed to, you still had another day to stay? Reporter: Here's Jones' explanation. I took my Downstairs and put it in the trunk. I think I went to 7-eleven or something for a soda. In the middle of the night? Not in the morning when you're checking out -- Because I wasn't sure when we were leaving, that day or the next day. Reporter: Still, a sympathetic jury might overlook those questionmarks and accept Jones' account, reducing this to a case of "He says" -- I did not hurt her in any Kind of way. Reporter: And "She can't really remember." The memory was not clear because -- it's -- probably because of -- I don't know. But this is the one opportunity that you have to be able to show to the jury, what a liar this person is. Even though he's calm and he's cool and he looks like he hasn't done a thing in the world, it was my job to be able to show that he's a liar. Reporter: So Brennan begins circling around that moment he believes is the key to the case -- the suitcase and the tell-tale tug. So, the only way is to draw him in little by little. Little by little. And that's what I did. I set him up, ask him some question, let him give some innocuous answer, and then I come back to it later. Well, let's -- let's back up a little bit. I said, well, you're here on the video, you're leaving. Where were you going? He says, oh, I was going out to my car. What stuff did you bring out to your car? All I had was my suitcase. Let me ask you this. What did you have in your bag when you went out to your car? My clothes. How much clothes did you have? Just a bunch of . I was there two weeks. How much stuff? Reporter: A pause. For the first time, Jones is jammed up. You could just see the wheels turning and he's saying, oh, I got to come up with a scenario. Why is this heavier than it appears to be? How much clothes, did you have bowling balls in it? Was it fairly light? It was heavy. I had my xbox in there. Xbox in there, anything else? Clothes? How many pairs of shoes? Clothes, books. You had books? How many books did you have? Oh, I had five of them. Oh, you had five books. How big were they? Oh, big novels. You're an avid reader? I read a lot. What kind of Reading do you do? Science fiction. Science fiction? Reporter: But then, this avid reader suddenly has a case of amnesia. What was the name of the books you were Reading? I have no idea. I couldn't tell what you the name of the book was I just took out of my pocket. Well, what's the book you've been Reading right now? I couldn't tell you. Reporter: By now, Brennan's had enough. Everything you're saying doesn't add up. It doesn't make sense. What doesn't make sense? Your timeline stinks. Your story stinks. The whole story stinks. Reporter: He's sure Jones is lying and more importantly, he believes any jury viewing this video will think so, too. Because any of the things he was talking about made absolutely no sense whatsoever. Who goes and leaves, takes their clothes out to the car two days before they check out? Nobody. Who is 6'4", wakes 380 pounds, has some underwear and an xbox in a suitcase and needs two hands to pull it out of a crack? Nobody. Doesn't make sense. Doesn't make sense because it's all . What is true is that he already beat this girl, he's dragging her out. He's gone for an hour because he's looking for a place to dump her because he thinks she's dead. Reporter: Maybe so, but throughout the interrogation -- Would you be willing to take a polygraph exam? Sure. Reporter: And a polygraph test right after. So, you don't know what happened to her or how it happened to her? No. Reporter: Jones maintains total innocence. He played his role right to the very, bitter end. Reporter: Jones is charged with sexual battery and kidnapping. But before any trial begins, the case against him will nearly fall apart. The defense is about to get a big assist from, of all people, the victim. I was afraid this guy was just going to get let off. He was going to walk.
This transcript has been automatically generated and may not be 100% accurate.