EDIT: Oh I just remembered another funny exception for “ch”: In “Chemistry” the “H” is neither pronounced nor does it modify the “C” to make the normal “ch” sound. It just sounds like there is a “C” there. Like “Cemistry.” Except looking at that, that pattern is used in something like “Cemetery” and then the “C” sounds like an “S”. I’m going to stop now because there are so many of these I could probably go on forever if I kept thinking about it.

That one’s the loanword problem. Greek has letters Κ (kappa) and Χ (chi, pronounced similar to “key” but from the back of the throat). Kappa is a close approximation to the English K, while chi doesn’t have anything like it in English. So loanwords from Greek that used chi are written differently.

Wall of random language knowledge coming:

In the Latin language, where our alphabet derives, C was originally always hard (like “calendar” as opposed to “celery”). When Greek loanwords entered Latin, kappa was transliterated to C (Kronos—Cronus). Chi, being similar but just a bit more breathy, was transliterated as Ch (Chimera).

Latin experienced pronunciation shifts and gradually branched off into the modern romance languages. In several of them, the letter C conditionally softened (e.g. cerveza in Spanish, cent in French, etc).

The Latin alphabet did not enter use for the English language until Christianity came to Britain in the middle ages. Before then, Old English, which should be more accurately called the Anglo-Saxon language, was written in Futhorc, a runic system like old Norse. The Latin alphabet was adapted to Anglo-Saxon, but there were not always 1:1 pronunciations, so pronunciation of certain letters shifted and some runic holdovers from Futhorc like Þ (thorn) for Th remained in use.

In the intervening centuries, Anglo-Saxon/English would undergo a pronunciation shift, a series of invasions from the Danes and Normans, and Ecclesiastical Latin (Latin after undergoing a pronunciation shift) remained present for religious purposes. All of these would introduce new loanwords and expand the English vocabulary at different times. The Germanic loanwords would be transliterated, while the Romantic loanwords would be lifted directly or edited slightly because they already used the same writing system. The softer Ch sound (like “chair”) existed in English by the time the Normans arrived, and they started writing it like Ch because that sounded closer to its use in French.

Finally, this was all further complicated by the invention of the printing press. By the time this occurred, the Latin alphabet became the de facto writing system for most of Europe, but languages did not quite meet 1:1 on which letters were used. Some innovations like the letter W stuck, because it was very convenient for German. And as it happens, the German printing presses invented by Gutenberg were the first to cross over into Britain. The German W was a convenient enough replacement for the English Ƿ (Wynn), but German had no equivalent for Þ (thorn) or Ð (eth, the th pronounced like “that”), so early English printers first approximated by using the letter Y for being less common and looking close enough (“ye old” is really “the old”) before eventually settling on Th.

Okay, one final note. On the random topic of W, and why it looks like two Vs, V is how U was written in classical Latin, and so W is double that. You’ll find the logic of W persists in a lot of words if you replace it with a U, even though we think of W as a consonant and U as a vowel. You can look at an edited word like “flouer” and potentially still read it as “flower” because we have other words like “flour” which have the same sound.