One way to increase the stakes in a conflict between your novel's protagonist and antagonist is to make the reader see that the villain thinks he's the hero of the story too. According to him, he's the good guy, doing the right thing. He might have a skewed idea of what the right thing is, but he can rationalize all his actions. He might even be right, once you shift your head into the correct mindset.
Here's a story that illustrates this principle. It's taken from real-life.
A friend of mine had a co-worker who was the office's champion bitch. She was a whip-cracking harridan to her underlings, demanding and unsympathetic to her equals, but the height of charm when the boss was around. She also had a habit of vilifying her co-workers in front of the boss to make herself look better. The woman was grasping and mercenary about promotions, bitter in temperment, uniformly hated by her co-workers, and completely unrepentant about any of it.
One day, during a coffee break, my friend--and she can't even remember why--started really talking to this woman.
It turns out, about fifteen years previous, the office bitch was a stay-at-home mum. One day, her husband--a police officer--went to work and didn't come home. He was killed on duty. Abruptly, this woman who had two small children and almost no job skills had to find a way to survive in spite of her grief.
And she did. She wrangled a job she wasn't really qualified for, then fought to be as good at it as humanly possible. She clawed after every opportunity for advancement because she needed the money, and she sacrificed herself--her life, her joy in life--for the sake of her kids. She kept her family together and even put her children through college.
Inside her own story, she's a hero.
To the people she works with, she's still the villain, although my friend never thought of her that way again.
When the reader can see that the villain isn't really such a bad guy, it increases the tension the reader feels because they do empathize with the villain a little. Remember that empathy means the reader sees themself in the character and subconsciously cheers on this reflection of themself. If they're cheering for the hero, but also cheering--even just a little bit--for the villain, then they're doubly invested in the story and doubly anxious about the story's climax and resolution. They know something bad is going to happen to at least one of the characters that their heart is paying attention to.
Have you ever turned a typical villain inside-out to show the reader how he sees himself as the hero? And if so, how did you do it? Also, describe how the villain in your current work-in-progress sees his or herself as the good guy of their own story ('cause they all do; even the evil overlords and psychotic serial killers.)
Figuring out the villain's rationale is sometimes the most fun part of designing your story's structure, and I'd love to hear how you handle it.