diff --git a/src/domain/reconstructionVerification.functionSources.test.ts b/src/domain/reconstructionVerification.functionSources.test.ts
new file mode 100644
index 0000000000..93e55d9e0e
--- /dev/null
+++ b/src/domain/reconstructionVerification.functionSources.test.ts
@@ -0,0 +1,554 @@
+import { describe, expect, it } from "vitest";
+
+import {
+  createEvidence,
+  parseEvidence,
+  type Evidence,
+  type EvidenceObservation,
+  type EvidenceProvider,
+  type EvidenceSubjectTarget,
+} from "./evidence.js";
+import { createEvidenceBundle, parseEvidenceBundle } from "./evidenceBundle.js";
+import { compareFunctions } from "./functionComparison.js";
+import { functionDossierSchema } from "./hopperValues.js";
+import {
+  jsonObjectSchema,
+  jsonValueSchema,
+  type JsonValue,
+} from "./jsonValue.js";
+import { verifyReconstruction } from "./reconstructionVerification.js";
+import { createResidualUnknown } from "./residualUnknown.js";
+
+const dossier = jsonValueSchema.parse(
+  functionDossierSchema.parse({
+    procedure: {
+      address: "0x1000",
+      name: "main",
+      signature: "int main(void)",
+      locals: [],
+    },
+    pseudocode: "return 0;",
+    assembly: [],
+    comments: [],
+    callers: [],
+    callees: [],
+    incoming_references: [],
+    outgoing_references: [],
+    referenced_strings: [],
+    referenced_names: [],
+    basic_blocks: [{ start: "0x1000", end: "0x1001", successors: [] }],
+  }),
+);
+
+const source = (
+  digit: string,
+  observation: Partial<EvidenceObservation> = {},
+  hasSubject = true,
+): Evidence =>
+  createEvidence(
+    hasSubject
+      ? {
+          path: `/fixture/function-${digit}`,
+          sha256: digit.repeat(64),
+          format: "file",
+        }
+      : undefined,
+    { id: "fixture", name: "Fixture function analysis", version: "1" },
+    {
+      operation: "analyze_function",
+      parameters: { procedure: "main" },
+      result: dossier,
+      confidence: "derived",
+      authority: "shipped-artifact",
+      ...observation,
+    },
+  );
+
+const left = source("1");
+const right = source("2");
+const extra = source("3");
+const singular = {
+  left_evidence_id: left.evidence_id,
+  right_evidence_id: right.evidence_id,
+};
+const plural = {
+  left_evidence_ids: [left.evidence_id],
+  right_evidence_ids: [right.evidence_id],
+};
+const provider = {
+  id: "rea-function-comparison",
+  name: "REA function comparison",
+  version: "1",
+};
+const baselineResult = compareFunctions(left, right);
+
+const comparison = (
+  parameters: Record<string, JsonValue>,
+  observation: Partial<EvidenceObservation> = {},
+  sources: readonly Evidence[] = [left, right],
+  identity: {
+    provider?: EvidenceProvider;
+    target?: EvidenceSubjectTarget;
+  } = {},
+): Evidence =>
+  createEvidence(identity.target, identity.provider ?? provider, {
+    predicateType: "rea.function-comparison",
+    operation: "compare_functions",
+    parameters,
+    result: jsonValueSchema.parse({
+      ...baselineResult,
+      dimensions: baselineResult.dimensions.map((dimension) => ({
+        ...dimension,
+        evidence_links: sources.map(({ evidence_id: id }) => id),
+      })),
+    }),
+    confidence: "derived",
+    authority: "analyst-inference",
+    evidenceLinks: sources.map(({ evidence_id: id }) => id),
+    ...observation,
+  });
+
+const specification = (evidence: Evidence, dimension = "pseudocode") => ({
+  name: "Function reconstruction",
+  claims: [
+    {
+      kind: "structural-function",
+      claim_id: "function",
+      title: "Function agrees",
+      comparison_evidence_id: evidence.evidence_id,
+      dimension,
+    },
+  ],
+});
+
+const admittedVerification = (
+  evidence: Evidence,
+  sources: readonly Evidence[] = [left, right],
+  dimension = "pseudocode",
+) => {
+  // Admission controls use newly hashed Evidence and a valid bundle, not a stale digest.
+  expect(parseEvidence(evidence)).toEqual(evidence);
+  const bundle = createEvidenceBundle([...sources, evidence]);
+  expect(parseEvidenceBundle(bundle)).toEqual(bundle);
+  return () => verifyReconstruction(specification(evidence, dimension), bundle);
+};
+
+const verify = (
+  evidence: Evidence,
+  sources: readonly Evidence[] = [left, right],
+) => admittedVerification(evidence, sources)();
+
+describe("function reconstruction source parameters", () => {
+  it.each([
+    ["singular", singular],
+    ["plural", plural],
+    ["coherent aliases", { ...singular, ...plural }],
+  ])(
+    "accepts %s and preserves exact sides and unrelated metadata",
+    (_name, parameters) => {
+      const evidence = comparison({
+        ...parameters,
+        context: { label: "retained", revision: 7 },
+      });
+      const before = JSON.stringify(evidence);
+      const result = verify(evidence);
+      expect(result.status).toBe("pass");
+      expect(result.claims.items).toMatchObject([
+        {
+          observed_status: "unchanged",
+          left_evidence_ids: [left.evidence_id],
+          right_evidence_ids: [right.evidence_id],
+        },
+      ]);
+      expect(JSON.stringify(evidence)).toBe(before);
+    },
+  );
+
+  it("preserves plural-only multi-ID sides and their ordering", () => {
+    const fourth = source("4");
+    const evidence = comparison(
+      {
+        left_evidence_ids: [extra.evidence_id, left.evidence_id],
+        right_evidence_ids: [fourth.evidence_id, right.evidence_id],
+      },
+      {},
+      [left, right, extra, fourth],
+    );
+    expect(
+      verify(evidence, [left, right, extra, fourth]).claims.items,
+    ).toMatchObject([
+      {
+        status: "pass",
+        left_evidence_ids: [extra.evidence_id, left.evidence_id],
+        right_evidence_ids: [fourth.evidence_id, right.evidence_id],
+      },
+    ]);
+  });
+});
+
+describe("function reconstruction source aliases", () => {
+  it.each([
+    ["no source declarations", {}],
+    ["missing right singular", { left_evidence_id: left.evidence_id }],
+    ["missing left singular", { right_evidence_id: right.evidence_id }],
+    ["missing right plural", { left_evidence_ids: [left.evidence_id] }],
+    ["missing left plural", { right_evidence_ids: [right.evidence_id] }],
+    [
+      "mixed left singular/right plural",
+      {
+        left_evidence_id: left.evidence_id,
+        right_evidence_ids: [right.evidence_id],
+      },
+    ],
+    [
+      "mixed left plural/right singular",
+      {
+        left_evidence_ids: [left.evidence_id],
+        right_evidence_id: right.evidence_id,
+      },
+    ],
+    [
+      "partial singular alias with plural pair",
+      { ...plural, left_evidence_id: left.evidence_id },
+    ],
+    [
+      "other partial singular alias with plural pair",
+      { ...plural, right_evidence_id: right.evidence_id },
+    ],
+    [
+      "partial plural alias with singular pair",
+      { ...singular, left_evidence_ids: [left.evidence_id] },
+    ],
+    [
+      "other partial plural alias with singular pair",
+      { ...singular, right_evidence_ids: [right.evidence_id] },
+    ],
+    [
+      "contradictory left alias",
+      { ...singular, ...plural, left_evidence_ids: [extra.evidence_id] },
+    ],
+    [
+      "contradictory right alias",
+      { ...singular, ...plural, right_evidence_ids: [extra.evidence_id] },
+    ],
+    [
+      "reversed aliases",
+      {
+        ...singular,
+        left_evidence_ids: [right.evidence_id],
+        right_evidence_ids: [left.evidence_id],
+      },
+    ],
+    [
+      "extra left alias ID",
+      {
+        ...singular,
+        ...plural,
+        left_evidence_ids: [left.evidence_id, extra.evidence_id],
+      },
+    ],
+    [
+      "extra right alias ID",
+      {
+        ...singular,
+        ...plural,
+        right_evidence_ids: [right.evidence_id, extra.evidence_id],
+      },
+    ],
+  ] satisfies [string, Record<string, JsonValue>][])(
+    "rejects %s after valid digest admission",
+    (_name, parameters) => {
+      expect(admittedVerification(comparison(parameters))).toThrow();
+    },
+  );
+});
+
+describe("function reconstruction malformed source IDs", () => {
+  it.each(
+    (
+      [
+        null,
+        false,
+        7,
+        "",
+        "ev_invalid",
+        [],
+        [left.evidence_id],
+        { id: left.evidence_id },
+      ] satisfies JsonValue[]
+    ).map((invalid) => ({ invalid })),
+  )(
+    "rejects malformed singular values $invalid without falling back to plural aliases",
+    ({ invalid }) => {
+      for (const field of ["left_evidence_id", "right_evidence_id"]) {
+        for (const aliases of [{}, plural]) {
+          expect(
+            admittedVerification(
+              comparison({ ...singular, ...aliases, [field]: invalid }),
+            ),
+          ).toThrow();
+        }
+      }
+    },
+  );
+
+  it.each(
+    (
+      [
+        null,
+        false,
+        7,
+        "",
+        left.evidence_id,
+        [],
+        ["ev_invalid"],
+        [null],
+        { id: left.evidence_id },
+      ] satisfies JsonValue[]
+    ).map((invalid) => ({ invalid })),
+  )(
+    "rejects malformed plural values $invalid even with valid singular aliases",
+    ({ invalid }) => {
+      for (const field of ["left_evidence_ids", "right_evidence_ids"]) {
+        for (const aliases of [{}, singular]) {
+          expect(
+            admittedVerification(
+              comparison({ ...plural, ...aliases, [field]: invalid }),
+            ),
+          ).toThrow();
+        }
+      }
+    },
+  );
+
+  it.each([
+    [
+      "same singular source on both sides",
+      { ...singular, right_evidence_id: left.evidence_id },
+    ],
+    [
+      "duplicate left plural source",
+      { ...plural, left_evidence_ids: [left.evidence_id, left.evidence_id] },
+    ],
+    [
+      "duplicate right plural source",
+      { ...plural, right_evidence_ids: [right.evidence_id, right.evidence_id] },
+    ],
+    [
+      "same plural source on both sides",
+      { ...plural, right_evidence_ids: [left.evidence_id] },
+    ],
+    [
+      "overlapping plural sides",
+      { ...plural, right_evidence_ids: [right.evidence_id, left.evidence_id] },
+    ],
+  ])("rejects %s with the existing uniqueness guard", (_name, parameters) => {
+    expect(admittedVerification(comparison(parameters))).toThrow(
+      /unique and two-sided/u,
+    );
+  });
+});
+
+describe("function reconstruction admission controls", () => {
+  it.each([singular, plural, { ...singular, ...plural }])(
+    "requires exact source closure for %j",
+    (parameters) => {
+      expect(
+        admittedVerification(
+          comparison(parameters, { evidenceLinks: [left.evidence_id] }),
+        ),
+      ).toThrow(/closure disagrees/u);
+      expect(
+        admittedVerification(
+          comparison(parameters, {
+            evidenceLinks: [
+              left.evidence_id,
+              right.evidence_id,
+              extra.evidence_id,
+            ],
+          }),
+          [left, right, extra],
+        ),
+      ).toThrow(/closure disagrees/u);
+      expect(admittedVerification(comparison(parameters), [left])).toThrow(
+        /Missing source Evidence/u,
+      );
+    },
+  );
+
+  it.each([
+    { operation: "inventory_artifact" },
+    { predicateType: "rea.process-capture" },
+  ])("rejects source observation type %j", (observation) => {
+    const wrong = source("1", observation);
+    const evidence = comparison(
+      { ...singular, left_evidence_id: wrong.evidence_id },
+      {},
+      [wrong, right],
+    );
+    expect(admittedVerification(evidence, [wrong, right])).toThrow(
+      /unexpected observation type/u,
+    );
+  });
+
+  it.each(["procedure", "pseudocode", "assembly", "basic_blocks"])(
+    "rejects a function dossier missing %s",
+    (field) => {
+      const incomplete = jsonObjectSchema.parse(dossier);
+      delete incomplete[field];
+      const wrong = source("1", { result: incomplete });
+      const evidence = comparison(
+        { ...singular, left_evidence_id: wrong.evidence_id },
+        {},
+        [wrong, right],
+      );
+      expect(admittedVerification(evidence, [wrong, right])).toThrow();
+    },
+  );
+
+  it.each([
+    { authority: "historical-reference" as const },
+    { confidence: "inferred" as const },
+  ])("keeps insufficient source authority unknown: %j", (observation) => {
+    const weak = source("1", observation);
+    const evidence = comparison(
+      { ...singular, left_evidence_id: weak.evidence_id },
+      {},
+      [weak, right],
+    );
+    expect(verify(evidence, [weak, right]).claims.items).toMatchObject([
+      {
+        status: "unknown",
+        observed_status: "unchanged",
+        limitations: expect.arrayContaining([
+          "Source Evidence lacks qualifying shipped-artifact authority.",
+        ]),
+      },
+    ]);
+  });
+
+  it("keeps a source without artifact identity unknown", () => {
+    const unbound = source("1", {}, false);
+    const evidence = comparison(
+      { ...singular, left_evidence_id: unbound.evidence_id },
+      {},
+      [unbound, right],
+    );
+    expect(verify(evidence, [unbound, right]).claims.items).toMatchObject([
+      {
+        status: "unknown",
+        limitations: expect.arrayContaining([
+          "Structural source artifact identity is unavailable.",
+        ]),
+      },
+    ]);
+  });
+
+  it("rejects selected-dimension citations outside comparison closure", () => {
+    const evidence = comparison(singular, {
+      result: jsonValueSchema.parse({
+        ...baselineResult,
+        dimensions: baselineResult.dimensions.map((dimension) =>
+          dimension.dimension === "pseudocode"
+            ? {
+                ...dimension,
+                evidence_links: [left.evidence_id, extra.evidence_id],
+              }
+            : dimension,
+        ),
+      }),
+    });
+    expect(admittedVerification(evidence, [left, right, extra])).toThrow(
+      /dimension cites Evidence outside comparison closure/u,
+    );
+  });
+});
+
+describe("function reconstruction evidence integrity", () => {
+  it.each([
+    { operation: "compare_artifacts" },
+    { predicateType: "rea.artifact-comparison" },
+    { confidence: "observed" as const },
+    { authority: "shipped-artifact" as const },
+  ])("rejects changed comparison identity or authority %j", (observation) => {
+    expect(admittedVerification(comparison(singular, observation))).toThrow(
+      /identity or authority disagrees/u,
+    );
+  });
+
+  it.each([
+    { ...provider, id: "other-comparison" },
+    { ...provider, name: "Other comparison" },
+    { ...provider, version: "2" },
+  ])("rejects comparison provider %j", (identity) => {
+    expect(
+      admittedVerification(
+        comparison(singular, {}, [left, right], { provider: identity }),
+      ),
+    ).toThrow(/identity or authority disagrees/u);
+  });
+
+  it("rejects an artifact-bound comparison", () => {
+    const evidence = comparison(singular, {}, [left, right], {
+      target: {
+        path: "/fixture/comparison",
+        sha256: "4".repeat(64),
+        format: "file",
+      },
+    });
+    expect(admittedVerification(evidence)).toThrow(
+      /identity or authority disagrees/u,
+    );
+  });
+
+  it("retains active source unknowns as a gating result", () => {
+    const evidence = comparison(singular);
+    const mutation = createEvidence(undefined, provider, {
+      predicateType: "rea.residual-unknown-mutation",
+      operation: "record_unknown",
+      parameters: {},
+      result: { action: "record" },
+      confidence: "derived",
+      authority: "analyst-inference",
+      evidenceLinks: [left.evidence_id],
+    });
+    const unknown = createResidualUnknown(
+      {
+        question: "Does the source analysis cover this function?",
+        severity: "high",
+        domain: "function-comparison",
+        supporting_evidence_ids: [left.evidence_id],
+        contradicting_evidence_ids: [],
+        required_authority: "shipped-artifact",
+        required_confidence: "observed",
+        required_environment: null,
+        recommended_probes: [],
+        relationships: [],
+      },
+      mutation.evidence_id,
+      null,
+    );
+    const result = verifyReconstruction(
+      specification(evidence),
+      createEvidenceBundle([left, right, evidence, mutation], [unknown]),
+    );
+    expect(result.claims.items).toMatchObject([
+      {
+        status: "unknown",
+        observed_status: "unchanged",
+        unknown_ids: [unknown.unknown_id],
+      },
+    ]);
+  });
+
+  it("separately rejects parameter tampering without a recomputed digest", () => {
+    const evidence = comparison(singular);
+    const tampered = { ...evidence, parameters: plural };
+    expect(() =>
+      verifyReconstruction(
+        specification(evidence),
+        createEvidenceBundle([left, right, tampered]),
+      ),
+    ).toThrow(/semantic identifier does not match/u);
+  });
+});
diff --git a/src/domain/reconstructionVerification.ts b/src/domain/reconstructionVerification.ts
index b9ce943bc7..1900c93bea 100644
--- a/src/domain/reconstructionVerification.ts
+++ b/src/domain/reconstructionVerification.ts
@@ -229,7 +229,12 @@ const sourceSides = (
   evidence: Evidence,
 ): { left: string[]; right: string[] } => {
   const parameters = evidence.parameters;
-  if (claim.kind === "behavioral") {
+  let singularSides: { left: string[]; right: string[] } | undefined;
+  if (
+    claim.kind === "behavioral" ||
+    (claim.kind === "structural-function" &&
+      ("left_evidence_id" in parameters || "right_evidence_id" in parameters))
+  ) {
     const parsed = z
       .object({
         left_evidence_id: evidenceIdSchema,
@@ -237,10 +242,15 @@ const sourceSides = (
       })
       .passthrough()
       .parse(parameters);
-    return {
+    singularSides = {
       left: [parsed.left_evidence_id],
       right: [parsed.right_evidence_id],
     };
+    if (
+      claim.kind === "behavioral" ||
+      !("left_evidence_ids" in parameters || "right_evidence_ids" in parameters)
+    )
+      return singularSides;
   }
   const parsed = z
     .object({
@@ -249,6 +259,14 @@ const sourceSides = (
     })
     .passthrough()
     .parse(parameters);
+  if (
+    singularSides !== undefined &&
+    (parsed.left_evidence_ids.length !== 1 ||
+      parsed.right_evidence_ids.length !== 1 ||
+      parsed.left_evidence_ids[0] !== singularSides.left[0] ||
+      parsed.right_evidence_ids[0] !== singularSides.right[0])
+  )
+    throw new TypeError("Function comparison source Evidence aliases disagree");
   return { left: parsed.left_evidence_ids, right: parsed.right_evidence_ids };
 };
 
diff --git a/tests/boundary/mcp/functionComparisonMcp.test.ts b/tests/boundary/mcp/functionComparisonMcp.test.ts
index 88610b6eb0..da07ca8a98 100644
--- a/tests/boundary/mcp/functionComparisonMcp.test.ts
+++ b/tests/boundary/mcp/functionComparisonMcp.test.ts
@@ -3,10 +3,134 @@ import { describe, expect, it } from "vitest";
 
 import { createTestBinarySession } from "../../fixtures/binarySession.js";
 import { FUNCTION_COMPARISON_EXAMPLE } from "../../../src/contracts/functionComparisonExample.js";
-import { createEvidence } from "../../../src/domain/evidence.js";
+import { createEvidence, parseEvidence } from "../../../src/domain/evidence.js";
+import { jsonObjectSchema } from "../../../src/domain/jsonValue.js";
 import { createServer } from "../../../src/server/createServer.js";
 import { observed } from "../../fixtures/analysisExecution.js";
 
+describe("function comparison reconstruction MCP integration", () => {
+  it.each([
+    { comparisonStatus: "unchanged", verificationStatus: "pass" },
+    { comparisonStatus: "changed", verificationStatus: "fail" },
+  ] as const)(
+    "verifies public $comparisonStatus function comparison as $verificationStatus",
+    async ({ comparisonStatus, verificationStatus }) => {
+      let providerLaunches = 0;
+      const session = createTestBinarySession(() => {
+        providerLaunches += 1;
+        throw new Error("Function verification must not launch a provider");
+      });
+      const left = FUNCTION_COMPARISON_EXAMPLE.left;
+      const right =
+        comparisonStatus === "changed"
+          ? FUNCTION_COMPARISON_EXAMPLE.right
+          : createEvidence(
+              {
+                path: "/tmp/function-unchanged",
+                sha256: "2".repeat(64),
+                format: "mach-o",
+              },
+              left.provider,
+              {
+                operation: left.operation,
+                parameters: left.parameters,
+                result: left.normalized_result,
+                confidence: left.confidence,
+                authority: left.authority,
+              },
+            );
+      const server = createServer(session, session);
+      const client = new Client({
+        name: "function-verification-test",
+        version: "1",
+      });
+      const [clientTransport, serverTransport] =
+        InMemoryTransport.createLinkedPair();
+      try {
+        await server.connect(serverTransport);
+        await client.connect(clientTransport);
+        const compared = await client.callTool({
+          name: "compare_functions",
+          arguments: { left, right },
+        });
+        expect(compared.isError).not.toBe(true);
+        const comparison = parseEvidence(
+          jsonObjectSchema.parse(compared.structuredContent).evidence,
+        );
+        expect(comparison.normalized_result).toMatchObject({
+          status: comparisonStatus,
+        });
+        expect(comparison.parameters).toEqual({
+          left_evidence_id: left.evidence_id,
+          right_evidence_id: right.evidence_id,
+        });
+        expect(comparison.evidence_links).toEqual(
+          expect.arrayContaining([left.evidence_id, right.evidence_id]),
+        );
+
+        const verified = await client.callTool({
+          name: "verify_reconstruction",
+          arguments: {
+            specification: {
+              name: "Function pseudocode comparison",
+              claims: [
+                {
+                  kind: "structural-function",
+                  claim_id: "pseudocode",
+                  title: "Pseudocode agrees",
+                  comparison_evidence_id: comparison.evidence_id,
+                  dimension: "pseudocode",
+                },
+              ],
+            },
+          },
+        });
+        expect(
+          verified.isError,
+          JSON.stringify(verified.structuredContent),
+        ).not.toBe(true);
+        const verification = parseEvidence(
+          jsonObjectSchema.parse(verified.structuredContent).evidence,
+        );
+        expect(verification.normalized_result).toMatchObject({
+          status: verificationStatus,
+          summary: {
+            total: 1,
+            passed: verificationStatus === "pass" ? 1 : 0,
+            failed: verificationStatus === "fail" ? 1 : 0,
+            unknown: 0,
+          },
+          claims: {
+            items: [
+              expect.objectContaining({
+                status: verificationStatus,
+                observed_status: comparisonStatus,
+                comparison_evidence_id: comparison.evidence_id,
+                left_evidence_ids: [left.evidence_id],
+                right_evidence_ids: [right.evidence_id],
+              }),
+            ],
+          },
+        });
+        expect(
+          session
+            .exportEvidenceBundle()
+            .records.find(
+              ({ evidence_id: id }) => id === comparison.evidence_id,
+            ),
+        ).toEqual(comparison);
+      } finally {
+        await Promise.allSettled([
+          client.close(),
+          server.close(),
+          session.close(),
+        ]);
+        expect(providerLaunches).toBe(0);
+      }
+    },
+  );
+});
+
 describe("function comparison MCP integration", () => {
   it("records linked comparison Evidence and its residual unknown", async () => {
     const session = createTestBinarySession(() => ({