<b>Theorem.</b> There is no chain of nowhere dense subsets of $\mathbb{R}$ whose union contains an interval.

Proof. Suppose there was such a chain $\{\ B_i \mid i\in I\ \}$, where $\langle I,\lt\rangle$ is a linear order and $i\lt j$ implies $B_i\subset B_j$. First, I claim that  this chain cannot have countable cofinality, since then we could find a countable cofinal subset of $I$, and the union of the $B_j$ from this cofinal subset would also contain an interval, violating the Baire category theorem. So every countable subset of $I$ is bounded. In this case, consider the set $Q$ of rational numbers $q$ in the interval from the union $\bigcup_i B_i$. Each of them appears in some $B_{i_q}$, and the set of all $i_q$ for $q\in Q$ is a countable set and hence bounded in $I$. Thus, there is some $j\in I$ beyond all $i_q$. So $B_j$ contains all those $q$ and thus is not nowhere dense. QED

Edit. As George pointed out in the comments, essentially the same argument establishes the full property:

<b>Theorem.</b> There is no chain of nowhere dense subsets of $\mathbb{R}$ whose union is non-meager. 

Proof. Suppose that $B_i$ for $i\in I$ is a chain of nowhere dense sets whose union $\bigcup_i B_i$ is non-meager. Again, we see that every countable subset of $I$ must be bounded, for otherwise the union would be a countable union of nowhere dense sets and hence meager. Since $\bigcup_i B_i$ is non-meager, it must be dense on an interval, and so it must have a countable subset $Q$ that is also dense on an interval. By the argument above, since $I$ has uncountable cofinality, this set $Q$ must be in some $B_j$ for large enough $j\in I$, contradicting that $B_j$ is nowhere dense. QED