The Ekpyrotic Universe Scenario is a proposed alternative to cosmological inflation in terms of addressing some of the problems of standard big bang cosmology, in particular in terms of providing a mechanism for generating fluctuations on length scales which today are cosmological. I will discuss the mechanism of structure formation and explain why the resulting spectrum of fluctuations is not scale-invariant (it has spectral index n=3) in the four-dimensional toy model of the Ekpyrotic scenario in which all but one of the moduli fields resulting from the higher dimensional Horava-Witten starting point are fixed. If more than one modulus field varies in time, cosmological fluctuations include both isocurvature and entropy modes. I will present a new formalism to discuss the mixing of these modes, and discuss how it might be possible to obtain a scale-invariant spectrum of fluctuations in this context.