There are a variety of flags available in Jets of Time. These configure the behavior of the randomizer. Usually, several are combined together into categories (aka flagsets or presets). This page describes the individual flags, while the categories page describes the most commonly used standard presets.
n, default) or Hard (
h) - Hard provides a buff to enemy stats. Normal is the default and makes no changes.
e), Normal (
n), Hard (
h) - Changes the amount and quality of loot dropped from enemies and chests. Hard item difficulty also adjusts the prices of some common items and reduces the starting money to 10,000.
g): This removes the ability to use most glitches used in vanilla speedruns.
b): Bosses that block progression items are buffed.
p): Rather than heading to Zeal, the pendant will become charged upon finishing the Trial and being warped to 2300 A.D
m): Characters will learn all their techs without needing to visit Spekkio at the End of Time.
cr): Enable the Chronosanity Category.
ro): Shuffles most bosses with slight buffs/nerfs.
z): Defeating Zeal 2 at the end of Black Omen will count as the win condition rather than needing to defeat Lavos.
c): The characters in Dactyl Nest and Proto Dome are made harder to unlock by requiring the Dreamstone and completion of the Factory, respectively.
q): Randomize numbers and extra effects on equipped items.
h): Randomize efficacy and/or effect of healing items.
ef): The Epoch will begin in 1000 AD (it's on the peninsula by the Magic Cave's location in 600), but without wings. To earn its wings, find the “Jets of Time” key item and bring it to Dalton at the Snail Stop in Porre.
spf), Mostly Random (
spm), Fully Random (
te), Balanced Random (
qflag. Turns off music entirely.
The Extra flags change up game play in interesting ways that don't quite fit with the other flag categories. Some of these bring back changes from older versions of the randomizer, and some are just a bit esoteric.
k): Designed mainly as a feature to be played alongside Chronosanity, in which Key Items may be (and usually are) hidden inside treasure chests as opposed to behind bosses. With this flag enabled, some chests will contain Bucket Fragments. Once enough Bucket Fragments are collected, the player may use the Bucket Gate at the End of Time to travel to 1999 and challenge Lavos without otherwise earning Go Mode.
When setting the numbers for a Mystery Seed, enter values between 0-100 to set the probability of that option being chosen. These are not strictly percentages, but if you make sure your numbers in a single set always add up to 100, you may use them that way if it's easier to understand. For each category of flags here (with the exception of “Flag Probabilities,” the contents of which are decided independently of one another), the probability of any flag being chosen is x/y, where x is the value entered for that flag and y is the sum of all values entered under that set of flags.