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 her 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.
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.
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.
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.
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.
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.
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.
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.
Skins
Gems sometimes can change their appearance in some levels; or as part of the Advent Calendar Event thanks to a Promo Code which changed the Gems Skin for a limited period of time.
| Skin | Black | Blue | Green | Pink | Red | Yellow |
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| Christmas Skin | 
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| Van Gogh Skin | 
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