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The two-dimensional Schoenflies theorem says that a simple closed piecewise linear curve in $S^2$ separates it into two components whose closures are piecewise linear balls of dimension two. In particular, a homeomorphism of the curve to the equator extends to a piecewise linear homeomorphism of the whole sphere.

A piecewise linear ball is a space piecewise linearly homeomorphic to a standard simplex. Write $D=B_1\cap B_2$. The complementary disk to $D$ in each $\partial B_j$ is a disk by the two-dimensional Schoenflies theorem. Thus each pair $(\partial B_j,D)$ is piecewise linearly homeomorphic to a sphere with a chosen hemisphere. Choose these boundary maps to agree on $D$. Extend them to the interiors by coning from an interior point, after compatible subdivisions. The resulting maps identify $B_1$ and $B_2$ with the two halves of a standard ball, glued along its equatorial disk. ConsequentlyThe same boundary parametrization proves a useful companion fact: if a ball is indented by removing a smaller ball attached along a boundary disk, the closure of what remains is again a ball. In the standard boundary-disk model, move the indented disk through a collar neighbourhood to a flat disk.

A handle decomposition is a filtration obtained by attaching handles $D^r\times D^{n-r}$ along $\partial D^r\times D^{n-r}$ in the boundary of the preceding stage. The number $r$ is the handle index; index-zero handles are disjoint balls, and index-$n$ handles close the remaining spherical boundary components. Starting with a triangulation of $M$, thicken its vertices, then its edges, and successively its higher-dimensional simplexes. In a barycentric subdivision these thickenings have precisely the indicated handle and attaching-region product structures. Adding collars between successive attachments gives a collared handle decomposition.

For a critical level handle embedding, assign successive distinct heights $t_j$ to the handles. At height $t_j$ the horizontal slice contains the $j$th handle and its attaching region. Between handle heights, the embedded boundary of the previously attached handles travels along its product collar; there is no topological change there. The lower boundary collar meets the attaching region of the next handle, and the upper collar leaves its new boundary. The stated ambient isotopy therefore separates all topology changes into horizontal handles and all intervening motion into collars. For an embedded surface, the local changes are the appearance of a disk, attachment of a band, and disappearance of a disk.

Here is the three-dimensional conclusion, with the distinction between the bounded and unbounded regions made explicit: a piecewise linear embedded $S^2$ in ${\mathbb{R}}^3$ bounds a piecewise linear three-ball; in the one-point compactification $S^3$, both complementary closures are three-balls. The unbounded closure in ${\mathbb{R}}^3$ itself is not a compact ball.

Put the embedded sphere in critical level handle embedding position. At a regular horizontal level its intersection with the plane is a finite disjoint union of simple closed curves. An innermost such curve bounds a planar disk whose interior misses the sphere. Cut the sphere along this curve and insert two slightly displaced copies of the disk. This replaces one sphere by two spheres. Repeat at regular levels between the critical heights, using innermost curves first. The number of curves at these chosen levels decreases at each operation, so the process stops. Each resulting sphere then lies in a slab containing at most one horizontal handle.

These terminal spheres bound balls directly. With no handle the surface is a disk transported through a collar and capped at its ends, the boundary of $D^2\times I$. A minimum or maximum merely supplies one of those caps. At a band level there are two planar boundary circles on one side and one on the other. Cap the two circles, straighten each planar disk using the two-dimensional Schoenflies theorem, and straighten the joining band in its planar collar. If the circles are not nested, this gives two balls joined along a boundary disk; if they are nested, it gives a ball with one boundary-attached ball removed. The gluing three-balls along a boundary disk argument and its indentation version show in both cases that the terminal sphere bounds a ball. This also explains why the planar position of the band matters: no assertion about an arbitrary knotted band is being made.

Reverse the disk surgeries. Suppose the two resulting spheres bound balls $A$ and $B$. Their disjoint boundaries imply that the balls are disjoint or one contains the other. Shrink the small displacement of the two surgery caps back to the original planar disk. In the disjoint case, the pre-surgery sphere bounds the union of two balls along that disk. In the nested case, it bounds the larger ball with the smaller boundary-attached ball removed. Both are balls by the preceding elementary facts. Induction through the finitely many surgeries proves the Three-dimensional Schoenflies theorem. To treat the other region in $S^3$, remove a point inside the ball just constructed and apply the same argument in the resulting copy of ${\mathbb{R}}^3$.

A 3-manifold is an irreducible three-manifold when every piecewise linear embedded two-sphere bounds a ball. Suppose $p:{\mathbb{R}}^3\to M$ is a universal cover, and lift an embedded sphere $S$ to $\tilde{S}$. Since $S$ is simply connected, its lift maps homeomorphically to $S$. By the Three-dimensional Schoenflies theorem, $\tilde{S}$ bounds a compact ball. The inverse image of $S$ is locally finite, so only finitely many other lifted spheres lie inside this ball. Choose an innermost one, bounding a ball $B$ whose interior meets no lift of $S$.

The interior of $B$ maps to one component $U$ of $M\setminus S$. This restriction is a covering map onto $U$: a path in $U$ starting in the image lifts into $\mathrm{int}B$, since it cannot cross a lifted boundary sphere. The covering is proper, because a compact subset of $U$ has preimage closed in the compact ball and cannot meet $\partial B$. Near $S$, the boundary map $\partial B\to S$ is one-to-one, so this connected covering has one sheet. The map on $B$ is therefore a homeomorphism onto $U\cup S$. Thus every embedded sphere in $M$ bounds a ball, and $M$ is an irreducible three-manifold.

A map between compact connected orientable irreducible 3-manifolds with nonempty boundaries, injective on the boundary and on the fundamental group, is homotopic to a homeomorphism relative to the boundary. The boundary determines degree $\pm 1$, and the cover corresponding to the image of the fundamental group consequently has one sheet. Straighten the preimage of an incompressible hierarchy surface, cut both manifolds, and repeat. At the terminal balls, extend the prescribed boundary homeomorphisms by coning. The homotopies and homeomorphisms glue across the straightened surface collars.

Suppose disjoint separating spheres cut a 3-manifold into pieces none of which is a punctured three-sphere. Compress one sphere along a disk disjoint from the others. The old sphere and the two new spheres enclose a three-times punctured sphere. At least one of the two pieces on the compressed side is not a punctured sphere; retain that new sphere and discard the other. The piece on its opposite side cannot become a punctured sphere, since capping its boundaries and applying the Three-dimensional Schoenflies theorem would make the original opposite piece a punctured sphere as well. Hence the number of spheres and the nontriviality condition can be preserved.