This puzzle initially seems to present a lot of information at once. We have five 5x5 square grids suspended on different levels or layers, tokens placed on these grids that come in a variety of shapes and colours, and blue and red lines drawn between different squares on each level. Of the token types, we have five different colours (red, yellow, green, blue, purple) and five different shapes (hearts, triangles, diamonds, spades, clubs), or 25 different kinds of tokens total. It is therefore reasonable to assume that we want to arrange these 25 different tokens somehow on each level, given each level has exactly 25 squares in its grid, and duplicate tokens appear in the puzzle on different layers. The next step then is to determine how exactly these 25 tokens should be arranged on the grids per level. The only information we have not yet used is the supplied red and blue lines. Looking at the top layer for help seems reasonable here since we are given five tokens on its grid, as opposed to the four supplied on every other level. Interestingly, the central token, a green spade, is connected by a blue line to the green heart, and by a red line to the yellow spade. The suggestion here is that a blue line is drawn between any two adjacent (including diagonally adjacent) squares whose tokens have the same colour, while a red line is similarly drawn between any two adjacent squares whose tokens have the same shape. This idea is supported by the fact no blue and red lines occupy the same space (or else the adjacent squares in question would have to host identical tokens) and that when at any point a threesquare Lshape is formed by lines of the same colour, its endpoints are also joined by that colour's line (since the endpoints are diagonally adjacent squares whose tokens must share the same colour/shape). Finally, the puzzle title, Characterisation, hints at us having to consider the characteristics of the various tokens. If we then follow these rules, it is possible to determine a unique configuration of the 25 tokens for each layer, as illustrated below (see the Addendum for general tips on how to derive the filledout layers): Thus far we have not used the positioning of these layers in solving any steps of the puzzle, so this fact seems like the best thing to consider next. The story text describes the levels as being contained with a cube, and similarly the perspective of the puzzle image suggests we want to imagine the layers to lie directly above/below each other. The logical step to take from here is to consider other slices of the cube  that is, to look at the 5x5 grids formed by slicing the cube in layers perpendicular to the levels we were previously working on. Doing so for the "side" slices of the cube (i.e. those slices facing left/right when looking at the "cube" headon) gives the following new grids, going from left to right: It should be fairly clear here that a letter is formed in each slice by a different colour; this is promising, since the title Characterisation somewhat hints at this (we are forming characters, or letters, by singling out certain characteristics). In fact, going from left to right, the letter is formed by the colours red, yellow, green, blue, and purple respectively  the natural rainbow colour ordering. Furthermore the letters we get are R, G, P, Y, B, which also happen to be the first letters of the colours used in the puzzle (red, green, purple, yellow, blue). However an arbitrary colour ordering does not seem to be enough to constitute an answer or an indication as to the next step. The next thing to do is consider those grids found by taking slices of the cube along its third axis, i.e. by considering those slices facing forward/back. From the front to the back slice, we get: It follows that from this different perspective, the characters should be formed by tokens of the same shape rather than colour. Although some of the letters here are less obvious, they should still be easily identifiable provided we can use some natural ordering of the different types of shape (just as the colours were ordered by rainbow order). The most obvious ordering is by increasing side/vertex number, namely heart (2 sides/corners), triangle (3), diamond (4), spade (5), club (6). By looking at the hearts in the first slice, the triangles in the second, etc., we obtain the letters S, D, C, T, H, which again correspond to the shape names (spades, diamonds, clubs, triangles, hearts). So now we have derived an ordered list of colours and an ordered list of shapes. Separately, these lists don't seem particularly helpful, but together they naturally suggest five particular tokens: the red spade, green diamond, purple club, yellow triangle, and blue heart. The final step then is to figure out what to do with this ordering of five particular tokens. Returning to the original grids (those with all 25 tokens per grid), the most logical thing to do is draw lines between the tokens in the order given (i.e. red spade  green diamond  purple club  yellow triangle  blue heart). This gives the following (from top layer to bottom): We have clearly drawn yet another set of characters, this time spelling out the word Rebus, which is itself a term meaning pictorial representations of words or characters. AddendumThere are many ways to deduce the positions of each token on each of the five grids/layers, but some of the more common techniques are listed here:

The answer is: rebus 
