Apologetics is not usually known for producing gripping fictional thrillers, but it does have a few. In fact, I think you might be surprised by how many novel apologetic works are out there. Here is a sampling. If you know of any others add it to the list below with a link to its amazon page.
1. A Skeleton in God’s Closet by Paul L. Maier
As far as I know this was the first (and one of the better imho) novels incorporating apologetics. Paul L. Maier is the professor of ancient history at Western Michigan University and has written and translated some important historical works such as Josephus: The Essential Works, Eusebius: The Church History, and In the Fullness of Time: A Historian Looks at Christmas, Easter, and the Early Church.
Amazon describes A Skeleton in God’s Closet: “When an ancient skeleton is discovered in Israel, will it shed new light on the life of Jesus or plunge the world into chaos?”
Dr. Jonathan Weber, Harvard professor and biblical scholar, is looking forward to his sabbatical year on an archaeological dig in Israel. But a spectacular find that seems to be an archaeologist’s dream-come-true becomes a nightmare that many fear will be the death rattle of Christianity.Carefully researched and compellingly written, A Skeleton in God’s Closet explores the tension between faith and doubt when science and religion collide. In the end, it’s a thought-provoking page-turner, driven by one man’s determination to find the truth―no matter the cost.”
I really thought Maier did a fine job on this work. I just happened to discover 
it for a dollar at a resale shop. The title caught my attention and I devoured it. It essentially explores what would happen to Christianity if we discovered that Jesus did not rise from the dead. He had two sequels to this volume: More Than a Skeleton and The Constantine Codex. More Than a Skeleton explores eschatology and the return of Jesus (it was my least favorite of this Skeleton series) and the Constantine Codex explores what would happen if we discovered missing manuscripts to the New Testament. Maier even gives cameo appearances of real scholars such as Daniel Wallace and Edwin Yamauchi in The Constantine Codex.
[Caveat] – Maier has also written two books in the historical fiction genre, but he likes to categorize it as a “documentary novel” because the former emphasizes the fiction o
ver the history (many times to the 
detriment to the history) while in his works he has devised a structure that only resorts to fiction to fill in the historical gaps. Essentially, he is a historian first and a novelist second, while most historical fiction is the other way around. He has done a fine job in both Pontius Pilate and The Flames of Rome. As the titles suggest Pilate is about the true story of how and why the crucifixion took place, from the perspective of the Roman politician who changed history. The Flames of Rome follows the family of Flavius Sabinus, the mayor of Rome under Emperor Nero, in order to capture the tension of the political conflict in Rome before the Great Fire.
2. Five Sacred Crossings: A Novel Approach to a Reasonable Faith by Craig Hazen
Craig Hazen, the director of the M.A. program in Christian Apologetics at Biola University and editor of the journal Philosophia Christi, wrote this quick read (168 pages) which has a nice plot while investigating worldview claims of other religions and philosophies.”Professor Michael Jernigan, a Christian, is teaching a religions course at a community college by using a rare text he owns—“The Five Crossings.” Each “Crossing” unveils a universal spiritual question, which only Christianity can satisfactorily address because it is testable, presents salvation as a free gift, paints a picture of the world that matches reality, makes a non-compartmentalized life possible, and has Jesus at the center.”Craig prefaces this novel in his introduction: Defenses [of Christianity] usually come from believing theologians, philosophers, lawyers, and scholars of various stripes. From time to time, however, scholars who are fascinated by presenting reasons for faith have used allegories, analogies, novels, and other modes of storytelling to make specific points about the truth of the Christian view of the world…. This present work certainly does not compare to what [C.S.] Lewis produced except that it fits in the same category of literature.”
3. The Lazarus Effect: A Novel by Ben Witherington III
This is a series of six books that doesn’t deal with apologetics proper, but it does touch on archaeology and biblical scholarship, which apologetics interacts with regularly. Ben Witherington III is professor of New Testament for Doctoral Studies at Asbury Theological Seminary and doctoral faculty at St. Andrews University, and the author of over thirty-five books. He begins this series with The Lazarus Effect. This work has been described as an archaeological thriller. Apparently, the protagonist of this series Art West is based on Ben’s grandfather, James Arthur West, who was also an archaeologist. West makes a discovery of a lifetime in Jerusalem finding the tombstone of Lazarus. This indicates that Jesus raised him from the dead, but the stone is stolen, sold to the British Library, and West is implicated in an antiquities fraud that will lead to a trial. Other books in this series includes: Roman Numerals, Papias and the Mysterious Menorah, Corinthian Leather, Roma Aeterna, and Ephesian Miracle.
4. The Coffee House Chronicles by Josh McDowell and Dave Sterrett
Dave Sterrett (who I am glad to say I know personally and taught with several years ago) teams up with Josh McDowell to produce this trilogy which follows Nick, a 
college freshman at a state school in Texas. Nick has his spiritual world turned upside-down with what he hears in an introduction to religion class. His questions turn into conversations as he dialogues with professors, friends, and family about the authenticity the Bible, the identity of Jesus, and the historicity of the resurrection. This series includes: Is the Bible True…Really?, Who Is Jesus…Really?, and Did The Resurrection Happen…Really?
which from the titles you can tell the topics of each book. Amazon: “The Coffee House Chronicles are short, easily devoured novellas aimed at answering prevalent spiritual questions. Each book in the series tackles a long-contested question of the faith, and then answer these questions with truth through relationships and dialogue in each story.”
5. The Owlings: A Worldview Novella and The Owlings: Book Two by Dan DeWitt
Dan DeWitt; dean of Boyce College and teaches courses on worldview, philosophy, apologetics, and C. S. Lewis; provides a short young adult story in which Josiah learns that the world is not all there was, is, or ever will be from the most unlikely visitors: Gilbert, a talking owl and three of his friends.
This series, deemed a “worldview adventure” continues in book two. Josiah returns with Gilbert the talking owl touching on moral themes like poverty, bullying, charity, sympathy, and the like, but its main goal is to demonstrate the limits of science.
6. The Chronicles of Adonai series by Braxton Hunter
Dr. Hunter is president of Trinity College of the Bible and Theological Seminary and professor of apologetics. He has written several books on apologetics proper such as Evangelistic Apologetics and Blinding LIghts: The Glaring Evidences of the Christian Faith. Active in the apologetics community, Hunter has debates and blogs on the Christian truth. and He has dipped his hand into apologetical fiction with his Chronicles of Adonai series. 
Set in a post apocalyptic dystopian society, all references and talk of God is removed by the leaders of the community call Adonai. A great review by Mark Evans reveals that Dr Hunter “includes the cosmological argument . . .the teleological argument . . . and the moral argument. . . . He also gives a clear explanation of the Gospel and repentance. There are some characters who respond to the Gospel. He also emphasizes the clearness of general revelation (Romans 1.20) Early on in the book one of the characters examines the purpose of all that exists.”
The series is in two volumes: The Colony and The Island.
7. The Testimonium by Lewis Ben Smith
One day as I walked into my local Half Price Books I stumbled upon Lewis Ben Smith, a local author who was personally selling his books at a side table. Lewis has been a high 
school history teacher for the past three decades at a private school in east Texas. An avid archaeologist, he routinely takes his classes out to tributaries to find arrowheads. In 2014 he published The Testimonium. This novel explores the questions: What if there were new findings that proved, in today’s science, that the resurrection of Jesus Christ is true? Smith’s focus is on the archaeology, but The Testimonium begins a series of books called The Capri Team Adventures which follows the excursions of a team of archaeologists as they uncover other earth shattering discoveries. Other titles in the series:
Matthew’s Autograph – The back cover description: “Finding the undisturbed tomb of one of 
the Apostles of Jesus leads the Israeli government to call in Duncan’s companions, who had discovered the Testimonium of Pontius Pilate three years earlier. When the three archeologists arrive in Tel Aviv, they discover an amazing document inside the tomb: the end of Matthew’s Gospel, written in the Apostle’s own hand! Excitement turns to pandemonium when they translate the scroll and find the text varies drastically from every copy of the Book of Matthew in existence. Have the New Testament Gospels been altered since they were written? Has this tomb really lain undisturbed for two thousand years? Is this ancient manuscript really . . . MATTHEW’S AUTOGRAPH?”
Gnostic Library – Smith’s most recent work concludes the Capri Team Adventures when the
archaeologists are captured by terrorists when they were investigating the manuscripts of the Gnostics found in Egypt. One Amazon reviewer states that The Gnostic Library is “A fast-paced, globe-spanning novel about human love and inhuman brutality, that mixes ancient history and modern headlines into an edge-of-your-seat thriller!”
