The level of the fortress is set by the level of the top players when the shield is dropped for the first time (and subsequently after each kill it is reset and set at the next dropping of the shield).
You can reduce the level of the fortress by the injection of the virus, up to 25 levels. The time it is reduced for that amount is set by how many injections of viruses are made. Up to 48 injections can be made (6 hubs x 8 players per hub) and needs to be carefully controlled to maximise the chances of killing the fortress. It is often useful to be in an alliance to learn how it is done and to watch and learn that way. You can often get into an alliance that is going to kill the fortress when the fortress has fallen 7 or 8 times already and the world is almost dead.