Doctor Who: Legacy's core combat mechanic involves the matching of colored gems on a 5x6 field. These gems take six colors—black, blue, green, pink, red, and yellow—five of which are keyed to the attacks of the various characters from which the player can build their team. Below is a breakdown of the six gem colors, what their associated strengths and weaknesses are, and what time fragments are needed to advance a character of the color to the next rank.
Red[]
- See also: Category:Red allies
Red gems activate the attacks of red characters. Red attacks against green targets deal double damage, while those against blue targets deal half damage. Red enemies are weak to blue attacks.
Blue[]
- See also: Category:Blue allies
Blue gems activate the attacks of blue characters. Blue attacks against red targets deal double damage, while those against green targets deal half damage. Blue enemies are weak to green attacks.
Yellow[]
- See also: Category:Yellow allies
Yellow gems activate the attacks of yellow characters. Yellow attacks against black targets deal double damage. Yellow enemies are weak to black attacks.
Green[]
- See also: Category:Green allies
Green gems activate the attacks of green characters. Green attacks against blue targets deal double damage, while those against red targets deal half damage. Green enemies are weak to red attacks.
Black[]
- See also: Category:Black allies
Black gems activate the attacks of black characters. Black attacks against yellow targets deal double damage. Black enemies are weak to yellow attacks.
Pink[]
Pink gems do not activate any attacks, but rather heal the party. Characters of various colors have the ability to shift gems of other colors to pink.
Stone[]
Stone gems appear only on certain levels, typically those involving the Weeping Angels. These gems can be cleared away in combos as normal, but do nothing aside from adding to the player's combo count. They can be turned into pink gems using the Third Doctor's Reverse the Polarity. Also, allies who can select a gem for conversion can change the color of Stone gems.
Secondary Color[]
Rank 5 allies have a secondary color. Each group of matching gems activates both primary attacks from allies with the corresponding primary color and secondary attacks from allies with the corresponding secondary color. Some allies have the identical primary and secondary color and both attacks will be activated simultaneously.
Damage against an enemy is calculated separately for a primary and secondary attack. For instance, Jenny (primary color red, secondary color blue) attacks an Ironside Dalek (green), the red attack will deal 200% damage, while the blue attack deals 50%.
There is currently a bug in the game where secondary attack receive damage boost from boost ability and wave enhance perk twice, for more details, please look take a look at Boost power and the Combo strength formula.
Summary[]
| Gem Color | 
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| Strong against | Green | Red | Blue | Black | Yellow | Heals allies | No effect |
| Weak against | Blue | Green | Red | N/A | N/A |
Skins[]
Gems sometimes can change their appearance in some specific levels or events. The first alternate skin was the Christmas one, which was the default skin for a limited time during December 2013, as part of the 2013 Advent Calendar. Since version 2.2 it is possible to select alternative Gem Skins in the "Settings" menu accessible through "Options". There's also a "Colorblind" skin for colorblind players, which is a mix of the other skins.
| Skin | Red | Blue | Yellow | Green | Black | Pink |
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| Default |
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| Christmas | 
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| Van Gogh | 
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| Beast | 
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| Dalek | 
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| Master | 
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| Ood | 
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| Silent | 
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| Roundels | 
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| Cybermen | 
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| Colorblind |
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| The 12th | 
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| Pixel | 
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| Snowflake | 
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| 2016Easter 1 | 
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| 2016Easter 2 | 
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| Halloween 1 | 
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| Halloween 2 | 
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The following is a list of levels featuring alternate gem skins. This substitution only happens if the Default skin is used. Skins outside from this list are only available by changing the default skin in the Options.
| Level | Season | Gem Skin |
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| No Black Gems: Old friends, older enemies part 2 | Chapter 2 | Christmas |
| Vincent and the Doctor | Chapter 3 | Van Gogh |
| (12th+, Clara+ req.)Sixty Six | Expert Levels | Roundels |
| Dark water | Season 8 | Cybermen |
| (10th+, River+, Strax+, Clara+ req.) Confusion | Expert Levels | Mixed skins |
| Seven Zygons Pixelated (L30 team req.) | 2014 Advent | Pixelated |
| (12th Doctor, Clara, Bessie) The Cyber King: Impact | Chapter 4 | Cybermen |
| Bubble Universe Echo - The Impossible Planet | Chapter 4 | Ood |
| Bubble Universe Echo - The Satan Pit | Chapter 4 | Beast |
| 2015 Christmas | Fan Area | Snowflake |
| (L40) A Very Zygon Halloween 2016 | Fan Area | Halloween 1 |