Let $M$ be an irreducible, orientable, open 3-manifold with finitely generated fundamental group, this gives us a Scott's Core $C\hookrightarrow M$ so that the inclusion is an homotopy equivalence and such that the ends of $M$ are in 1-1 correspondence with the components of $M\setminus int(C)$.
Let $\mathcal E$ be an end and $\partial_{\mathcal E} C$ be the boundary component facing it. I want to show that the inclusion $\partial_{\mathcal E} C\hookrightarrow Z$, for $Z$ the component of $M\setminus int(C)$ containing $\mathcal E$, is an isomorphism on $H_1$.
I can get surjectivity but I fail to get injectivity.
$H_i(M,C)=0$ by assumption that the inclusion of $C$ is a homotopy equivalence. Now use excision on the interior of $C$ to see that $H_i(M \ \text{int }C,\partial C)=0$. But $(M \setminus \text{int } C,C)$ is the disjoint union of the spaces you're interested, and (relative) homology is additive under disjoint union, hence all of your groups are zero.
(If one is pedantic they say "You need the set you're excising to have closure contained in $C$! But just take a tubular neighborhood of the boundary etc.)