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Put $A=T^2\setminus B^2$ and let $E=\partial A=S^1$ denote the attaching circle. The version of the Seifert-van Kampen theorem used here states that if $X=U\cup V$ is an open cover with $U,V,U\cap V$ path-connected and a common base point in $U\cap V$, thenThe expression on the right means the pushout of groups of the two inclusion-induced group homomorphisms; they need not be injective.

Choose a thin collar neighbourhood $C_A$ of $E$ inside $A$, and a thin equatorial band $C_S$ inside $S^2$. For example, before the square's side identifications take $C_A=\{v:1\le |v|<1+ϵ\}$ with $0<ϵ<1/2$, and take $C_S=\{(x,y,z)\in S^2:|z|<ϵ\}$. In the glued topological space setThese are open subsets: their preimages in the two pieces are open and respect the gluing. They cover $X$, and the three deformation retractionsfix $E$. Thus all three spaces are path-connected, and a base point $b\in E$ is preserved.

For completeness, the fundamental group of a once-punctured torus is $F(a,b)$, and its boundary loop of a once-punctured torus represents $[a,b]=ab{a}^{-1}{b}^{-1}$, up to orientation and a change of base point. Here is the geometry behind both facts. In the square model, move each point of $A$ radially outwards to the square boundary:The denominator never vanishes on $A$. The homotopy stays outside the missing open disk, stays inside the square, and fixes the square boundary, so it descends through the side identifications. The resulting retract is a wedge of two circles. Its fundamental group is the free group on the two oriented side based loops $a,b$. The inner boundary loop travels around the square once under this deformation retraction; its successive sides read $a,b,a^{-1},b^{-1}$.

The sphere $S^2$ is simply connected. Hence the group homomorphism from ${\pi }_1(E)\cong \mathbb{Z}$ to ${\pi }_1(V)$ is trivial, while its map to ${\pi }_1(U)$ sends a group generator to $[a,b]$. Applying the Seifert-van Kampen theorem givesThe final group isomorphism follows because the single relator makes $a,b$ commute, leaving the free abelian group on two group generators. The two hemispheres kill the same boundary loop; they do not create another group generator.