MWC99 consists of two phases. In the first phase (the Qualifying Round, or QR), teams will be seeded into pools of 5-7 teams. The pools will be named after different Myth II units (e.g. "Trow" and "Warlock"). Over the course of the QR, each team will play a match against every other team in their pool, round-robin style. After the completion of the QR, a number of teams from each pool will advance to the second phase, the Double Elimination (DE) ladder. The exact number of teams to advance will depend on the number of participants in the tournament, and may include "wildcard" teams as needed to fill out the DE ladder. During the DE ladder, teams will be paired against other teams to play one or two matches per week. Winners continue to advance up the ladder to play against other undefeated teams in the "Top Bracket," while losers move to a parallel "Bottom Bracket" to compete against other teams with one defeat. In subsequent rounds, newly-defeated teams move to the Bottom Bracket, while teams that lose a match in the Bottom Bracket are eliminated from the tournament. At the conclusion of the DE phase, the MWC99 championship will be decided in a Grand Final between the winners of the Top and Bottom Brackets.

More detailed information can be found in the Qualifying Round and Double Elimination Rules.

Seeding is the process of ranking competitors according to their approximate skill level to facilitate a roughly even distribution of ability in the initial population of pools or elimination brackets. The number 1 seed is, in a sense, the "favorite" to win the tournament. The phrase "higher-seeded team" refers to the team that was initially ranked (or seeded) higher than the other. For example, when comparing the number 1 seed and the number 12 seed, the number 1 seed is the higher-seeded team.

Seeding will be used to distribute teams into pools for the Qualifying Round. The results of the Qualifying Round will be used to re-seed the teams that survive the Qualifying Round and populate the Double Elimination Ladder.