The game revolves around a young man named Daniel Garner, who is happily married to his wife Catherine. At the start of the game, Daniel is about to take Catherine out for a birthday meal. As they drive towards their destination at high speed, in the pouring rain, Daniel takes his eyes off the road to look at his wife and While his attention is diverted, he ploughs their car into a truck. Both of them are killed instantly in the crash. While Catherine manages to make it to Heaven and lives in harmony, Daniel is trapped in Purgatory. One day meeting an accomplice called Samael, he is told that in order to receive purification, he has to kill four of Lucifer's generals in order to prevent a war between Heaven and Hell. Lucifer has been secretly organising a massive army that could overwhelm Heaven, taking over Purgatory in the process. Small portions of the army are already beginning the march. With little choice available to him, Daniel accepts the task. With the forces of Hell seizing and corrupting various parts of Purgatory, Daniel goes through different and random phases of history within Purgatory, which range greatly from ancient times to the modern era. These include Medieval Europe, Babylon, the Crusades, 1800s and even a time slice of modern industry.
After killing the first general, Daniel meets a woman named Eve, another soul who has been in Purgatory for a long time. She gives him information about the whereabouts of the remaining generals and small elements of Lucifer's army already mobilising. She also tells him about life in Purgatory, and the possibility that he could be dragged to Hell should he fall in battle and become lost forever. While this is all understood, what Daniel does not understand is why he came here, but Eve insists it is because of something in his past, and it is up to him to find out.
After the second general and reuniting with Eve, Daniel travels to meet a demonic friend named Asmodeus, for information about new rallying positions for Lucifer's armies. Asmodeus once saved Daniel's life after he single-handedly defeated four demons at once one day, almost losing himself in the process. Eve is wary of Asmodeus and questions as to why he did not finish Daniel when he was weak, but he insists that he did not come to Purgatory to fill the graves with lost souls like the others. He also questions Eve if she is really "The Eve" referenced in the Bible, in which Daniel jokes "Where is Adam?" before continuing on.
After the third general, he confronts Samael, having had enough of the fighting and wanting out of Purgatory, but Samael remains firm with Daniel that it is not that simple to leave and he must finish the task given to him. After being directed to the whereabouts of Alastor, Lucifer's right-hand and final general, Daniel is warned Alastor is already aware that he is being pursued and his own elite soldiers are prepared and waiting. Daniel reluctantly continues his quest for purification.
After Daniel kills Alastor, Eve arrives at the scene in shock, realising Lucifer will no doubt be on his way and they should make themselves ready. Surprisingly, Asmodeous arrives, complimenting Daniel for his victory and examining the scene. Suddenly, both Eve and Daniel find Asmodeus highly suspicious and try questioning him as to why he is really in Purgatory, in which he eventually replies, "I didn't come here to fill graves; I dig them." Suddenly, he dissolves into a ball of fire and Lucifer himself appears. He mocks Daniel while recognising him as a worthy opponent and thanking him for removing Alastor, who had been constantly arguing with Lucifer that the armies should have attacked sooner rather than wait. He snatches Eve, whom he claims had escaped from hell, and takes her with him before disappearing back into Hell.
Samael appears, congratulating Daniel for his success and informs him his task is done. Now he may proceed to Heaven and reunite with Catherine. But Daniel refuses, knowing that it is not over yet, "not even close" to use his words. He also knows that it would be only a matter of time before Lucifer can fledge a new and massive enough army, but the next time would be far worse. He decides to go after them, but Samael tries to make him reconsider, for if Daniel goes to hell, there will be no escaping from there. Daniel turns down the offer once more and asks that Catherine be told not to wait for him, for he will not be coming. Samael gives in and shows him the direction to the gates of hell, warning that they are protected by the most elite of the demonic forces for the purpose of keeping the souls of those who are damned within Hell.
Daniel eventually emerges in hell, a twisted landscape made of torn fragments from history. After vanquishing enough souls of the damned, most of which are recognisable as foes he has defeated, he confronts Lucifer in Demon Mode and kills him, rescuing Eve in the process, who has been rendered unconscious. After killing Lucifer, Alastor reappears before him, with hordes of demons around him. Daniel learns that he did not really kill Alastor and that he could only be defeated in Hell. With Lucifer gone, the position of Hell's ruler is open. Alastor has already taken it and announced his ultimatum. He leaves Daniel to the mercy of the demons around him, who eagerly accepts the challenge. The game ends with Daniel defending himself against the never-ending hordes. Daniel's adventures continue in Painkiller: Battle Out of Hell.
If the game is finished in Trauma (the hardest difficulty in the game which has to be unlocked by playing Nightmare), an alternate ending is presented at the end of Chapter 4 after Daniel kills Alastor. He is now finally able go to Heaven and reunite with Catherine at last. (Apparently, the idea here is that after having defeated Lucifer and found Alastor revived and leading the forces of Hell at the end of Chapter 5 on Nightmare difficulty, Daniel finishes his quest by killing Alastor a second time on Trauma difficulty. Nevertheless, this Trauma ending is arguably not canon because it would obviate all the other Painkiller games.)
Main article: Levels
The game consists of five Chapters, each of which consist of a varying number of levels (but not more than six). Unlike for many first-person shooters, the level menu gives the player the option of re-playing levels, which he might want to do under certain circumstances. Most often, this would be if he failed to earn the Tarot card the first time he played the level. Or, he may lack enough gold pieces to play the Tarot cards he did earn.
The game takes place in Purgatory. The exact location is a mystery, but it appears to be a parallel universe version of Earth (sometimes Daniel is outside at night, and the moon is the same one that Earth has) where various Earth structures appear unchanged, albeit decaying and with no normal inhabitants or functioning society. Instead, Daniel is assaulted by hordes of enemies sent to harass him, which may vary from zombies, monsters that resemble different kinds of human soldiers and ninjas, to more exotic sorts, including large crustacean-looking things and witches on broomsticks.
The levels in the first Chapter have a primarily cemetery feel, where the enemies are mostly types of zombies, with the overall air being of a broken, ruined civilization from ages past. With Chapter 2, it switches to a more modern, 20th century feel, featuring soldiers, ninjas, and zombies on the different levels. Chapter 3 continues the modern feel and concentrates on various types of soldiers as the enemy. Chapter 4 returns to the old civilization feel, whereas Chapter 5 (and the Hell level in particular) features a mix of everything.