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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 normal surface meets each tetrahedron in disjoint disks of the four triangular and three quadrilateral types. Its arcs in a face join distinct edges, each disk meets an edge at most once, and at most one quadrilateral type occurs in a tetrahedron. These last requirements exclude, for example, a disk with an octagonal boundary.

We first establish the surgery operation needed for the sphere system. Suppose a disk $D$ disjoint from the other spheres compresses one sphere $S$. It produces spheres $S^{\prime }$ and $S^{\prime \prime }$. Small parallel copies of the three spheres bound a three-times punctured three-sphere $P$. Denote the old piece on the uncompressed side by $A$, and the two pieces on the compressed side by $B^{\prime }$ and $B^{\prime \prime }$. If both $B^{\prime }$ and $B^{\prime \prime }$ were punctured three-spheres, then $P$ glued to them would also be a punctured three-sphere, contrary to the hypothesis on the original cut manifold. Choose, say, $B^{\prime }$ which is not of this type, and retain $S^{\prime }$ alone in place of $S$.

The other new piece is $A\cup P\cup B^{\prime \prime }$. It too cannot be a punctured three-sphere. If it were, cap its external boundary spheres to make $S^3$. All the spheres separating $A$ from the attached pieces then bound three-balls by the Three-dimensional Schoenflies theorem; the component containing $A$ would be a punctured three-sphere, contradicting the hypothesis on $A$. Thus the sphere surgery preserving nontrivial complementary pieces keeps exactly $k$ spheres and keeps every complementary piece nontrivial. The assumption that all spheres separate ensures that the old and new pieces used here really are distinct sides.

Apply general position to the whole sphere system, avoiding the vertices and making it transverse to edges and faces. We describe a terminating normalization, allowing the replacement operation just proved as well as isotopy. If some component of its intersection with a tetrahedron is not a disk, choose a boundary circle innermost among circles not bounding such disk components. A disk just inside the tetrahedral boundary gives a compression; if intervening disk components occur, first push them into collars of their boundary disks. Perform the compression and retain one new sphere as above. This replaces a non-disk tetrahedral piece by disk pieces without increasing edge intersections. Repetition is finite: every compression divides the original sphere along a separating circle, and the sum of $1-\chi$ over the non-disk planar tetrahedral pieces decreases; disk components can then be put in boundary collars. A closed sphere component wholly in a tetrahedron is impossible, because it would cut off a three-ball, contrary to the complementary-piece condition.

Now each tetrahedral piece is a disk. A face circle innermost in a face allows its incident disk to be moved through that face disk, removing the circle. This reduces the number of face intersections without increasing the edge weight. A returning face arc similarly gives an edge bigon across which the surface can be pushed, reducing the number of edge intersections by two. Restore tetrahedral disk pieces by the preceding operations whenever necessary.

It remains to exclude multiple intersections of a disk with an edge, which the absence of returning face arcs alone does not exclude. Suppose a tetrahedral disk meets an edge twice. Among such disks choose a pair of intersections consecutive on the edge and with no other surface intersection between them. Such a pair exists: an intervening disk crosses the edge interval an even number of times, so passing to an innermost intervening pair eventually gives consecutive points. Join them by an arc in the disk. The disk pieces divide the tetrahedron into three-balls, and this arc together with the edge interval lies in the boundary of one of these three-balls. It therefore bounds a bigon with interior disjoint from the surface. Push across the bigon to reduce edge weight by two. At fixed weight the previous moves reduce face and non-disk complexity; the edge weight itself is a nonnegative integer. Hence the whole process terminates. A final tetrahedral disk meets each edge at most once, and its boundary separates either one vertex from three or two vertices from two. It is respectively a normal triangle or quadrilateral. Thus a normal system of exactly $k$ spheres with the required complementary-piece property exists.

For the finite decomposition, we need a bound on such normal systems, not merely an assertion that they have been normalized. Let $f_2$ be the number of faces of the fixed triangulation. In a triangular face cut by normal arcs, all but at most four complementary regions are rectangles between adjacent parallel arcs. Thus at most $4f_2$ complementary three-dimensional components contain a nonrectangular face region. Every remaining component is assembled from product regions between parallel normal disks, so is an interval bundle whose boundary components are spheres. Its connected base is either $S^2$ or ${\mathbb{RP}}^2$. The product $S^2\times I$ is a punctured three-sphere, and is excluded. The other possibility is the twisted interval bundle over ${\mathbb{RP}}^2$, namely ${\mathbb{RP}}^3$ with a three-ball removed. Each such piece contributes a distinct ${\mathbb{F}}_2$ summand to $H_1(M;{\mathbb{F}}_2)$: gluing along spheres does not identify first-homology classes, by the Mayer–Vietoris sequence. Since $k$ separating spheres give $k+1$ components, we obtain the explicit finite bound

For an arbitrary closed connected $X$, first cut out nonseparating spheres. A neighbourhood of one such sphere together with an arc joining its two sides is a punctured $S^2$-bundle over $S^1$; the bundle is the product or the twisted bundle according to the orientation of the attaching identification. Its complement is connected, so this extracts a connected sum factor. The mod-two first Betti number of the remaining capped manifold decreases by one. Hence only finitely many such extractions are possible. The remaining manifolds have only separating spheres.

Whenever a remaining factor is not a prime three-manifold, split it along a sphere into two factors neither homeomorphic to $S^3$. Viewed in the original remaining manifold, all these successive splitting spheres form a disjoint system whose pieces are not punctured three-spheres. The normalization and bound just proved prohibit infinitely many such splittings. This proves existence of a finite prime decomposition, including for $X$ without assuming orientability.

For completeness, both sphere bundles extracted above are prime three-manifolds. Their fundamental group is $\mathbb{Z}$, so a separating sphere and the van Kampen theorem express $\mathbb{Z}$ as a free product in which one capped factor has trivial fundamental group. Its punctured piece lifts homeomorphically to the universal cover $S^2\times \mathbb{R}$, identified with ${\mathbb{R}}^3\setminus \{0\}$. That compact lifted piece has one spherical boundary and must be the bounded side of this sphere in ${\mathbb{R}}^3$. It misses the origin, so the Three-dimensional Schoenflies theorem makes it a three-ball. The corresponding capped factor is $S^3$, as required.

Suppose now that $X$ is orientable. A prime factor which is not an irreducible three-manifold contains a nonseparating sphere: an essential separating sphere would already split it nontrivially. Extracting the corresponding sphere bundle shows that the factor must be $S^2\times S^1$. Thus the other nontrivial primes are irreducible.

Consider two prime decompositions. Represent each by a sphere system, including one nonseparating sphere in each $S^2\times S^1$ factor. The capped pieces are now the irreducible factors and copies of $S^3$. Make the two sphere systems transverse. To remove their intersections, choose a circle innermost on a sphere of the second system and surger the first system along its disk. Retain both surgery spheres temporarily. The old sphere and the new pair bound a three-times punctured sphere; adding the pair and then deleting the old sphere only inserts or removes spherical punctures.

This operation cannot alter an irreducible capped piece: every new sphere in that piece bounds a three-ball, so it can only split off a punctured $S^3$ piece. The other pieces were already punctured $S^3$, where the same conclusion follows from the Three-dimensional Schoenflies theorem. After small displacements the surgery removes the chosen intersection circle and introduces none. Repeat until the sphere systems are disjoint. Their union is a common refinement, and its non-$S^3$ capped irreducible pieces are precisely those of each original decomposition. Hence these factors agree, up to order and orientation-preserving homeomorphism.

Finally, the number $r$ of $S^2\times S^1$ factors is determined bywhere the sum runs over the common irreducible factors. This uses additivity of first homology under connected sum, not a claim that the fundamental group determines a manifold. Therefore the orientable prime decomposition is unique up to order and insertion or deletion of $S^3$ factors.

The sphere $\{p\}\times S^2$ in $S^1\times S^2$ is nonseparating: its complement is $(S^1\setminus \{p\})\times S^2$, which is connected. A sphere bounding a ball separates, so this product is not an irreducible three-manifold.

To show it is prime, suppose a separating sphere cuts it into compact pieces $V,W$ with one spherical boundary each. The Seifert-van Kampen theorem givesA free product of two nontrivial groups is nonabelian: choose nonidentity elements in the two factors; their products in the two orders are distinct reduced words. Hence one factor, say ${\pi }_1(V)$, is trivial. The inclusion of this simply connected compact piece lifts to the universal cover $\mathbb{R}\times S^2\cong {\mathbb{R}}^3\setminus \{0\}$. The lift is an embedding: equality of lifted points would imply equality of their projections in $V$. Its image $\tilde{V}$ is compact with boundary the lifted sphere.

Use the three-dimensional Schoenflies theorem: a locally flat embedded sphere in ${\mathbb{R}}^3$ bounds a ball, and its compact side is that ball. The interior of $\tilde{V}$ is both open and closed in the corresponding complement component, and compactness rules out the unbounded component. Thus $\tilde{V}$ is the bounded ball, and $V$ itself is a ball. Capping $V$ gives $S^3$, so every connected-sum decomposition is trivial. Therefore $S^1\times S^2$ is prime but not irreducible.

Now let a prime closed connected orientable $M$ fail irreducibility. A sphere not bounding a ball cannot separate: if it did, primeness would make one capped side $S^3$, and the three-dimensional Schoenflies theorem would make its uncapped side a ball. Thus there is a nonseparating sphere $S$. Its two-sided neighborhood is $S^2\times [-1,1]$. Since the complement is connected, join its two boundary spheres by an embedded arc in that complement and thicken the arc. The union is a punctured $S^2\times S^1$: the thickened arc joins the two ends of the sphere-cylinder, and the remaining boundary is one sphere. This is the nonseparating sphere gives a sphere-circle summand construction and yieldsThe product is not $S^3$, since its fundamental group is $\mathbb{Z}$. Primeness forces $N\cong S^3$, soThe background results used are van Kampen, the explicit universal cover of the product, and the locally flat three-dimensional Schoenflies theorem; no Poincaré-conjecture argument is needed.

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.