There could be uncountably many irrationals not in $\bigcup_{k-1}^{\infty} I_k$ (depending on $\varepsilon$ of course). To see this, let $ \lambda$ denotes the Lebesgue measure on $[0,1]$. Then $\lambda I_k = \frac{\varepsilon}{2^{k-1}}$. Then it would follow that $ \lambda(\bigcup_{k\in\mathbb{N}} I_k) \leq \sum_{k \in \mathbb{N}} \lambda(I_k) = \varepsilon \sum_{k \in \mathbb{N}} \frac{1}{2^{k-1}} = 2\varepsilon$. Since $\varepsilon$ is arbitrary, this is a contradiction.