The Miller's Prologue is the first "quite" that occurs in the tales (to "quite" someone is to make repayment for a service, the service here being the telling of stories).
While Nicholas and Alison lie together, the foppish and fastidious parish clerk, Absolon, who is also attracted to Alison and believes her husband to be away, appears kneeling at the bedchamber's low "shot-wyndowe" (privy vent) and asks Alison for a kiss. In the darkness, she presents her "hole" (bottom) at the window and he "kissed her naked arse full savorly," pausing only when he feels bristly hair. He realizes the prank and goes away enraged. He borrows a red hot coulter (a knife-like plough part) from the early-rising blacksmith. Returning, he asks for another kiss, intending to burn Alison. This time Nicholas, who had risen from bed to "pisse" in the privy, sticks his own backside out the window and farts in Absolon's face. The enraged suitor thrusts the coulter "amidde the ers" burning Nicholas' "toute" (anus) and the skin "a hands-breadth round about". In agony, Nicholas cries for water, awakening John. Hearing someone screaming for water, he thinks that the Second Flood ("Nowel's Flood" as he calls it, confusing Nowel (Christmas) with Noah) has come, panics, and cuts himself down, falling to the floor and breaking his arm. The rest of the town awakens to find him lying in the tub. He tries to explain what he's doing in the tub, and sure enough in accordance with Nicholas' prophecy, he is considered a madman, and a cuckold too.
Some critics see Christian symbolism in the Miller's Tale. Parts of the tale are similar to the Annunciation, with Nicholas as the Angel Gabriel and Alison as Mary, while the clueless carpenter John is Joseph. Nicholas's singing of the 'Virgin's Angelus', a popular song about the Annunciation, hints at the parallel.
The character of Absolon introduces another theme of the Tales, the corruption of the Church. The Nun's Priest's Tale and The Shipman's Tale deals with the same theme; the Summoner, Friar and Pardoner personify it. Absolon is a clerk, but thinks of little except wooing young women at church:
3339: This Absolon, that jolif was and gay,
Gooth with a sencer (censer) on the haliday,
Sensynge the wyves of the parisshe faste;
And many a lovely look on hem he caste,
And namely on this carpenteris wyf.
Alison, however, does not return Absolon's affections, although she readily takes his gifts.
A third theme, that of knowledge and science, appears in several marginal comments. Nicholas is an avid astrologer (as Chaucer himself was), equipped with, "His Almageste, and bookes grete and smale, / His astrelabie, longynge for his art..." John the carpenter represents unintellectual laymen; John tells Nicholas:
3454: Men sholde nat knowe of goddes pryvetee [God's private affairs].
Ye, blessed be alwey a lewed [unlearned] man
That noght but oonly his bileve kan! [who knows nothing except the Creed]
He also recounts a story (sometimes told of Thales) of an astrologer who falls into a pit while studying the stars. The issue of whether learned or unlearned faith is better is also relevant to The Prioress' Tale and The Parson's Tale.
For example, in "The Knight's Tale", the two knights longed to just touch the princess but in "The Miller's Tale", both of the men get intimate with the woman, Nicholas in bed and Absolon kissing her "arse". In another parody, Absolon gets both a face-full of buttocks and a fart for his attempted wooing of Alison.
Chaucer refers to the Distichs of Cato with this passage: "He knew nat Catoun, for his wit was rude." The Distichs of Cato was one of the most common textbooks in schools throughout medieval Europe, and was familiar to most anyone with a basic education in Latin.