All participants in MWC99 must be using the latest version of MythII (currently 1.3). Updaters are available on the MWC99 Hotline Server.

All MWC99 games are scored by looking exclusively at the postgame stats screen (as this is available from a film file). There are a few exceptions that are detailed in the specific game rules (Capture the Flag, Assassin), but in general this is the case.

All games in MWC99 are scored using a point system. Each game type has a different system for awarding points, based on different accomplishments during the game. The winner of a game is the team that scores the most points in that game. In the Qualifying Round, the winner of a match is the team that wins more individual games. However, in the Elimination Rounds the winner of a match is the team that scores more points during the match. Points scored during the Qualifying Round matches are used to assist in seeding the DE ladder (see the section on Tournament Organization for more information). Once the DE phase begins, points are used only to determine the winners of matches. Teams should be sure to understand how points will be awarded for the games in a match before they play.

Some of the scoring rules depend on fractions, e.g. in Territories a team might receive two points per 3 flags that they own, or 1 point per 10% of their force remaining. In all such cases, the points awarded are rounded down. Thus a team with 5 flags in Territories has 3 + 2 flags; they receive two points for their set of 3 flags, and no points for their set of 2 flags.

In most MWC99 games, points are awarded for control or tagging of flags and balls at the end of the game. In any of these types of games, if the game ends due to the complete elimination of one force, the victorious force receives credit for tagging or control of all flags/balls in the game, regardless of whether or not they actually tagged or controlled them when the game prematurely ended.

Balls may be pushed by units anywhere on the mesh without restriction. However, using explosives or other means to put balls out of reach of all units available on a mesh is forbidden. Using explosives to move balls is allowed, but if the ball lands in an uncontestable position (in the opinion of the Triumvirate) the ball will be judged to be uncontrolled (if the Triumvirate judges the infraction was accidental) or to be captured by the opposing team (if the Triumvirate judges the infraction was intentional).

It is possible for sudden death to be extended indefinitely (e.g. by a stygian knight/soulless faceoff). If this occurs, the game can be ended by mutual consent of both teams by Yelling to each other. One team should withdraw to allow the game to end normally. Credit for items (balls, flags) that were contested to perpetuate the sudden death is divided evenly between the teams. Items that happened to be contested briefly during SD, but which were not part of the standoff, will not be divided. If the teams cannot mutually agree to end the game, after five minutes of unproductive sudden death have elapsed, any team's captain may Yell that they are asking for a division of the balls and withdraw to end the game. The Triumvirate will review the film and if the Triumvirate agrees that the standoff was genuine, credit for the balls will be divided. Otherwise, the results of the film will stand.