So it's worth pointing out off the bat that 'Dark Ages' is a fairly outdated and ahistorical term; typically Late Antiquity and Early Medieval are more accurate terminology.

There are really two interconnected but distinct concepts at play here, which really are problematic moreso in the Late Medieval period, rather than in what we'd associate with the 'Dark Ages.' The real crux of the issue is the Catholic doctrine that everybody, essentially, is sinful. From around the Seventh Century, the Church developed the idea of the continuing need for the repentance of sin and the penance to make up for it as one of the central doctrines of the Catholic Christian faith. Throughout the Early Medieval period, penance becomes increasingly codified through 'Penitentials' such as the Paenitentiale Theodori or the Scrifboc, with the concept of sins essentially becoming pseudo-legal infractions, with specific 'punishments' intended for the penitent to show contrition for their actions. In the Paenitentiale Theodori, for example, a free man who works on a Sunday should fast for seven days from ale or meat in order to show contrition for his sins.

In a similar vein, unless you manage to secure a deathbed confession and manage penance before you snuff it, it follows conceptually that everybody dies having committed at least a little bit of sin. Herein arises the concept of Purgatory which, even if not so named until the 12th Century, is at least implied in earlier theology. In essence, those souls which are not condemned to hell must atone for those sins for which they have not carried out penance in order to gain access to heaven. It was commonly held that saints or other holy figures could intercede on behalf of the dead who were deserving of help in order to speed their passage through purgatory and into heaven, and that this intercession could be achieved through prayer or the granting of an 'indulgence'. For example, Urban II declared that going on Crusade was an inherently penitential act, and that anybody who died on Crusade essentially went straight to heaven. Far more common was the saying of intercessory prayers for the departed. These were prayers which commended the souls of the dead to God, and frequently beseeched a saint or other figure to, in essence, put in a good word with God to fast-track somebody's progress into heaven. The best way to ensure these prayers were said after death was, basically, to hire somebody to say them; it was common to bequeath land or wealth in a will to a local religious institution in return for them saying intercessory prayers on your behalf after death. Some monarchs or wealthy nobles even established religious communities or sponsored new chapter houses directly in the hope that these would benefit them posthumously.

From the tenth century onwards, penitentials increasingly feature the concept that acts of penance can be boosted by the carrying out of benevolent or devout acts: Penitentials increasingly suggested that, for example, a necessary period of fasting could be shortened by going on a pilgrimage or a donation to a religious community. By the thirteenth century, these 'indulgences' were becoming increasingly conflated with the remission of temporal punishment rather than canonical penance; that is, that through monetary donation or other benevolent act, one would not just lessen the need for physical penance, but that one could forgo the need for any physical act of penance altogether and, in essence, fast track one's way into heaven. While the Church maintained that genuine contrition was still necessary and one could not excuse a mortal sin, nor was this a 'license to sin', the system became increasingly abused in the Late Medieval Period.

While Church doctrine maintained that officially, indulgences could only be granted as part of a right of penance alongside actual confession and contrition, they were increasingly seen as a commodity. Unscrupulous 'pardoners' frequently promised that they could, in essence, sell you salvation. While this ran contrary to actual Church doctrine, many clergy were convinced to turn a blind eye by the steady stream of revenue such individuals brought in to the Church. Even contemporaries regarded the situation as highly suspect: the pardoner in Chaucer's Canterbury Tales is a bitter satire of the corrupt nature of such figures in the 14th Century.

The Church did make periodic efforts to limit the practice but its attempts were hamstrung by its sheer effectiveness as a source of revenue and things frequently spiralled back out of control. Boniface IX publicly condemned the selling of indulgences to 'the simple-minded faithful' in the 14th Century, but was undermined by his own practice of selling religious offices in England to his favourites, prompting the English Parliament to vote in a royal veto of Papal authority. Indulgences became ever increasingly divorced from their original role as a supplement to penance and became seen as a means to 'pay off' sin instead. Famously the 'Butter Tower' of Rouen Cathedral, erected in the early 16th Century, was funded by donations from diocesans to prematurely excuse themselves from having to forgo butter during Lent.

This idea, that financial payment could now be used not only to forgo the physical act of penance but to actually preclude penance at all, was one of the driving factors of the Protestant reformation.