We can use the result of
gb = FullSimplify[
GroebnerBasis[{x == (r + (t + d Cos[a]) Cos[b]) Cos[c],
y == (r + (t + d Cos[a]) Cos[b]) Sin[c],
z == (t + d Cos[a]) Sin[b], w == d Sin[a],
Cos[c]^2 + Sin[c]^2 == 1, Cos[b]^2 + Sin[b]^2 == 1,
Cos[a]^2 + Sin[a]^2 == 1}, {x, y, z, w},
{Cos[c], Sin[c], Cos[b], Sin[b], Cos[a], Sin[a]}]]
to yield the implicit Cartesian equation for the $3$-torus:
t4[d_, r_, t_][x_, y_, z_, w_] = First[gb];
(Some people seem intimidated by the use of GroebnerBasis[]
, but here its only purpose is for eliminating parameters. Here's a simpler example of its use: First[GroebnerBasis[{x == Cos[t], y == Sin[t], Cos[t]^2 + Sin[t]^2 == 1}, {x, y}, {Cos[t], Sin[t]}]] == 0
, which yields the equation of a circle.)
We can then slice this torus with a hyperplane parametrized by its normal and its distance from the origin, like so:
With[{d = 10, t = 5, r = 1, (* radii *)
nrm = Normalize[{1, -1, 1, -1}], h = 4 (* hyperplane parameters *)},
ContourPlot3D[(t4[d, r, t][\[FormalX], \[FormalY], \[FormalZ], \[FormalW]] /.
Thread[{\[FormalX], \[FormalY], \[FormalZ], \[FormalW]} ->
RotationTransform[{nrm, {0, 0, 0, 1}}][{x, y, z, h}]]) == 0 // Evaluate,
{x, -15, 0}, {y, -15, 15}, {z, -15, 15},
BoundaryStyle -> Opacity[1/2, Gray], BoxRatios -> Automatic,
ContourStyle -> Opacity[3/4, ColorData["Legacy", "Mint"]],
Lighting -> "Neutral", MeshStyle -> {Red, Green, Blue}, PlotPoints -> 20]]

To appreciate this approach, contrast this with a low-dimensional version:
t3[p_, q_][x_, y_, z_] := (x^2 + y^2 + z^2 + p^2 - q^2)^2 - 4 p^2 (x^2 + y^2)
With[{p = 3, q = 1, nrm = Normalize[{1, -2, 3}], h = 1},
{ContourPlot[(t3[p, q][\[FormalX], \[FormalY], \[FormalZ]] /.
Thread[{\[FormalX], \[FormalY], \[FormalZ]} ->
RotationTransform[{nrm, {0, 0, 1}}][{x, y, h}]]) == 0 // Evaluate,
{x, -5, 5}, {y, -5, 5}, AspectRatio -> Automatic,
ContourStyle -> Directive[AbsoluteThickness[2], ColorData[1, 1]]],
ContourPlot3D[t3[p, q][x, y, z] == 0, {x, -5, 5}, {y, -5, 5}, {z, -5, 5},
BoundaryStyle -> Directive[AbsoluteThickness[2], ColorData[1, 1]],
Mesh -> None, RegionFunction -> Function[{x, y, z}, nrm.{x, y, z} < h]]}
// GraphicsRow]

Here's a less spherical-looking cross-section of a different $3$-torus, with a convenient cut-away to display the inner structure:
With[{d = 9, t = 6, r = 3, nrm = Normalize[{1, 3, 1, 3}], h = 2},
ContourPlot3D[(t4[d, r, t][\[FormalX], \[FormalY], \[FormalZ], \[FormalW]] /.
Thread[{\[FormalX], \[FormalY], \[FormalZ], \[FormalW]} ->
RotationTransform[{nrm, {0, 0, 0, 1}}][{x, y, z, h}]]) == 0 // Evaluate,
{x, -16, 16}, {y, -16, 16}, {z, -16, 16},
BoundaryStyle -> None, BoxRatios -> Automatic,
ContourStyle -> Directive[ColorData["Legacy", "PowderBlue"],
Specularity[2/3, 20]],
Lighting -> "Neutral", MaxRecursion -> 1,
MeshStyle -> Map[Directive[GrayLevel[1/10], Glow[#], Specularity[1, 15]] &,
{Magenta, Orange, Cyan}],
Method -> {"TubePoints" -> 20}, PlotPoints -> 15,
RegionFunction -> Function[{x, y, z}, x < 0 || y > 0 || z < 0]]] /.
Line[pts_, rest___] :> Tube[pts, 0.1, rest]
