There are many changes from Gemcraft Chapter 1 to Gemcraft Chapter 0. These changes are shown below. A major change from the original game was the replacement of water trenches with traps. Traps can only be set on the path; gems inside traps are five times weaker than in towers, but they attack twice as fast and their special ability is amplified as well. Also, there are 16 more Skills avaliable in Chapter 0 than in Chapter 1.

There are also many different modes you can play each level, which are unlocked after your wizard level gets to a certain point. There are ten modes total, counting the normal mode. You must complete a level on normal mode before any other mode. Three out of the eight other modes provide triple experience, allowing you to level up quicker on those modes. Beyond Corruption never gives you triple experience. Note: Heroic, Bleeding Edge and Arcane sometimes have giant monsters where the game says that these modes have none. The ten modes are:

  • Normal - Kill all the monsters (No requirements)
  • Sudden Death - If a monster reaches your wizard tower, you lose (obtained at Level 8)
  • Endurance - Survive for as long as you can (obtained at Level 16)
  • Heroic - +20% number of monsters, +40% monster hit points, No giant monsters, 2 additional waves (obtained at Level 24)
  • Swarm - Only swarm waves, +60% number of monsters (obtained at Level 32)
  • Time Siege - Kill all monsters before time runs out (obtained at Level 40)
  • Bleeding Edge - +60% number of monsters, +80% monster hit points, no giant monsters, 4 additional waves (obtained at Level 48)
  • Carapace - Only armored waves, Increased monster armor, reduced speed, +100% number of monsters, 6 additional waves (obtained at Level 56)
  • Arcane - +80% number of monsters, +100% monster hit points, no giant monsters, 8 additional waves, Monsters led by an Arcane Guardian (obtained at Level 64)
  • Beyond Corruption - 6 gems of grade 5 given at the start, +100% number of monsters, +150% monster hitpoints, no giant monsters, 10 additional waves with an increase of 2 waves after each victory (obtained after you've beaten the last level.)

Another change in Gemcraft 0 is the addition of a detailed banishment system. Every time a monster get banished, the next time it gets banished, the banishment cost will be 1.5 times the value of its previous banishment cost. For example, the first Arcane Guardian has a banishment cost of 2,000 mana first lap. For the second lap the banishment cost is 3,000 mana, 4,500 for the third lap, 6,750 for the fourth lap, etc.

A new feature introduced in Chapter Zero is the use of shrines. Shrines are powerful towers with an unknown origin, although they cannot be built. A shrine is activated by sacrificing a gem on it. The higher grade the gem, the more powerful the shrine burst is. Each shrine can only be activated a limited number of times (which is shown on each level). There are eight types of shrines in Gemcraft Chapter 0. They are:

  • Charged Bolt shrine - Releases charged bolts that crawl towards the monsters
  • Gem Transmute shrine - Changes all pure gems in your inventory to the color of the sacrificed gem. Gives damage bonus to transmuted gems. Only pure gems can activate this shrine
  • Experience shrine - Boosts your score gain
  • Anger shrine - Deals damage proportional to the sacrificed gem's grade to every monster in the field and halves available mana
  • Flash beam shrine - Damages all the monsters directly above, below, left and right of itself, taking away a portion of their hit points
  • Mana tap shrine - Increases the mana pool capacity and mana gain rates, and provides mana for every monster present on screen
  • Special damage shrine - Hits at most 100 monsters on screen with the sacrificed gem's special effect (only blue, green and cyan gems can activate this shrine)
  • Armor piercing shrine - Decreases the armor level of at most 100 monsters on screen by a set percentage proportional to the sacrificed gem's grade

The last change to challenge the player is the introduction of Beacons. Beacons are objects that are designed to help the monsters and make your job more difficult. They can only be destroyed by a grade 3 or higher gem. The types of beacons are:

  • Tower Defier beacon - towers cannot be built in the beacon's radius
  • Trap Defier beacon - traps cannot be built in the beacon's radius
  • Healing beacon - restores a portion of all nearby monsters' hit points
  • Shield beacon - shields all nearby monsters from all kinds of damage for several seconds

The game keeps eight gems types like the original game, but also includes the option to create prismatic gems, which are combinations of all eight gems. A minor change from the first game is that only part of the map is revealed to start with, and the rest of map appears after getting to a certain point.

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