Independent sets in graphs, i.e., subsets of vertices where no two are adjacent, have long been studied, for instance as a model of hard-core gas. The $d$-dimensional hypercube, $\{0,1\}^d$, with the nearest neighbor structure, has been a particularly appealing choice for the base graph, owing in part to its many symmetries. Results go back to the work of Korshunov and Sapozhenko who proved sharp results on the count of such sets as well as structure theorems for random samples drawn uniformly. Of much interest is the behavior of such Gibbs measures in the presence of disorder. In this direction, Kronenberg and Spinka [KS] initiated the study of independent sets in a random subgraph of the hypercube obtained by considering an instance of bond percolation with probability $p$. Relying on tools from statistical mechanics they obtained a detailed understanding of the moments of the partition function, say $\mathcal{Z}$, of the hard-core model on such random graphs and consequently deduced certain fluctuation information, as well as posed a series of interesting questions. In particular, they showed in the uniform case that there is a natural phase transition at $p=2/3$ where $\mathcal{Z}$ transitions from being concentrated for $p>2/3$ to not concentrated at $p=2/3$. In this article, developing a probabilistic framework, as well as relying on certain cluster expansion inputs from [KS], we present a detailed picture of both the fluctuations of $\mathcal{Z}$ as well as the geometry of a randomly sampled independent set. In particular, we establish that $\mathcal{Z}$, properly centered and scaled, converges to a standard Gaussian for $p>2/3$, and to a sum of two i.i.d. log-normals at $p=2/3$. A particular step in the proof which could be of independent interest involves a non-uniform birthday problem for which collisions emerge at $p=2/3$.