Normally in a Hilbert system, writing a proof $\Delta \vdash \varphi_n$ with lines $\varphi_1, \varphi_2, ..., \varphi_n$ is done such that each $\varphi_k$ is either a proposition contained in $\Delta$, an axiom of the Hilbert system, or the result of modus ponens on two earlier lines.
In natural deduction, how does this work when we now have no axioms to work with, but rather only rules of inference? Each line could either be the result of a rule, or an element contained in $\Delta$... is that all? Does natural deduction ultimately require a non-empty $\Delta$ in order for us to even write proofs?
Natural deduction systems generally have a notion of assumption introduction and discharge. The easiest-to-understand rule that needs this is $\to$-introduction. This says that if we can assume $A$ and then prove $B,$ then we can infer $A\to B$ and discharge the assumption $A,$ leaving us with an unconditional proof of $A\to B$ (i.e. a proof from the empty set).
The exact nature of how the rules work and the proofs are laid out varies from system to system. For instance, see the hypothetical derivations section of the wikipedia page.
A couple more things