diff --git a/clients/web/src/test/core/jsonUtils.test.ts b/clients/web/src/test/core/jsonUtils.test.ts
index e71b1e30..6c46a7e6 100644
--- a/clients/web/src/test/core/jsonUtils.test.ts
+++ b/clients/web/src/test/core/jsonUtils.test.ts
@@ -245,6 +245,42 @@ describe("JSON Utils", () => {
       });
     });
 
+    it("keeps a converted argument named __proto__ (#2123)", () => {
+      const protoNamed: Tool = {
+        name: "proto-named",
+        inputSchema: {
+          type: "object",
+          properties: Object.fromEntries([["__proto__", { type: "number" }]]),
+        },
+      };
+      const converted = convertToolParameters(protoNamed, {
+        ["__proto__"]: "3",
+      });
+      expect(Object.hasOwn(converted, "__proto__")).toBe(true);
+    });
+
+    it("reads an array type as a set when branches agree (#2123)", () => {
+      const setTyped: Tool = {
+        name: "set-typed",
+        inputSchema: {
+          type: "object",
+          anyOf: [
+            {
+              type: "object",
+              properties: { v: { type: ["number", "null"] }, a: {} },
+            },
+            {
+              type: "object",
+              properties: { v: { type: ["null", "number"] }, b: {} },
+            },
+          ],
+        },
+      };
+      // The same declaration written in the other order — not a disagreement,
+      // so the coercion survives.
+      expect(convertToolParameters(setTyped, { v: "2" })).toEqual({ v: 2 });
+    });
+
     it("leaves an ambiguously typed argument uncoerced (#2123)", () => {
       const ambiguous: Tool = {
         name: "ambiguous",
@@ -293,8 +329,9 @@ describe("JSON Utils", () => {
           ],
         },
       };
-      // Both spell the type the same way, so it is not ambiguous.
-      expect(convertToolParameters(arrayTyped, { v: "2" })).toEqual({ v: "2" });
+      // Both spell the type the same way, so it is not ambiguous — and the
+      // nullable declaration collapses to `number`, which is what coerces.
+      expect(convertToolParameters(arrayTyped, { v: "2" })).toEqual({ v: 2 });
     });
 
     it("ignores a malformed branch declaration when matching constants (#2123)", () => {
diff --git a/clients/web/src/test/core/nullableUnion.test.ts b/clients/web/src/test/core/nullableUnion.test.ts
index 24592e24..48b4a9bb 100644
--- a/clients/web/src/test/core/nullableUnion.test.ts
+++ b/clients/web/src/test/core/nullableUnion.test.ts
@@ -774,6 +774,16 @@ describe("admitsNull", () => {
       expect(admitsNull({ const: null, anyOf: [false] })).toBe(false);
     });
 
+    it("treats core identifier keywords as asserting nothing", () => {
+      // `$defs` declares subschemas for reference; it constrains nothing on its
+      // own, so this branch is unconstrained and admits null.
+      expect(admitsNull({ const: null, anyOf: [{ $defs: {} }] })).toBe(true);
+      // `$ref` is different — it applies whatever it points at.
+      expect(admitsNull({ const: null, anyOf: [{ $ref: "#/$defs/T" }] })).toBe(
+        false,
+      );
+    });
+
     it("does not override a sibling that rejects null", () => {
       // `const` is conjunctive with its siblings, not an override: both of
       // these reject every value, so claiming nullability would let the
diff --git a/core/json/jsonUtils.ts b/core/json/jsonUtils.ts
index 147a6180..040917aa 100644
--- a/core/json/jsonUtils.ts
+++ b/core/json/jsonUtils.ts
@@ -1,4 +1,5 @@
 import type { Tool } from "@modelcontextprotocol/client";
+import { normalizeNullableUnion } from "./nullableUnion.js";
 import {
   narrowBySuppliedNames,
   resolveRootUnion,
@@ -220,8 +221,11 @@ function coercionProperties<T extends RootUnionSchema>(
 function typeNameOf(schema: unknown): string {
   if (typeof schema !== "object" || schema === null) return "";
   const { type } = schema as { type?: unknown };
+  // Sorted: JSON Schema reads an array `type` as a SET, so `["number","null"]`
+  // and `["null","number"]` are the same declaration and must not read as a
+  // disagreement that drops the property from the coercion map.
   return Array.isArray(type)
-    ? type.join(",")
+    ? [...type].map(String).sort().join(",")
     : typeof type === "string"
       ? type
       : "";
@@ -262,7 +266,15 @@ export function convertToolParameters(
   const { base, branches } = resolveRootUnion(tool.inputSchema ?? {});
   const properties = coercionProperties(base, branches, params);
   for (const [key, value] of Object.entries(params)) {
-    const paramSchema = properties[key] as ParameterSchema | undefined;
+    const declared = properties[key];
+    // Collapsed first: a nullable declaration (`type: ["number","null"]`, or an
+    // `anyOf` with a null branch) states its real type on the surviving branch,
+    // and `convertParameterValue` dispatches on a single `type` string — so
+    // without this a nullable number is sent as the string it was typed as.
+    const paramSchema =
+      typeof declared === "object" && declared !== null
+        ? (normalizeNullableUnion(declared) as ParameterSchema)
+        : (declared as ParameterSchema | undefined);
 
     // A `const` the supplied text names is sent as the schema's own typed
     // value, not as the text: a branch pinned to `const: 2` is selected by
@@ -270,13 +282,21 @@ export function convertToolParameters(
     // rejects. Only an exact match is substituted — anything else is the
     // user's input and is left alone.
     const pinned = (paramSchema as { const?: unknown } | undefined)?.const;
-    if (pinned !== undefined && String(pinned) === value) {
-      result[key] = pinned as JsonValue;
-    } else if (paramSchema) {
-      result[key] = convertParameterValue(value, paramSchema);
-    } else {
-      result[key] = value;
-    }
+    const converted =
+      pinned !== undefined && String(pinned) === value
+        ? (pinned as JsonValue)
+        : paramSchema
+          ? convertParameterValue(value, paramSchema)
+          : value;
+    // `defineProperty`, not assignment: `__proto__` is a legal argument name —
+    // a discriminator can carry it — and assigning it would invoke the legacy
+    // prototype setter instead of putting it in the call.
+    Object.defineProperty(result, key, {
+      value: converted,
+      writable: true,
+      enumerable: true,
+      configurable: true,
+    });
   }
 
   return result;
diff --git a/core/json/nullableUnion.ts b/core/json/nullableUnion.ts
index fd6761dc..9232abdd 100644
--- a/core/json/nullableUnion.ts
+++ b/core/json/nullableUnion.ts
@@ -440,6 +440,15 @@ const ANNOTATION_ONLY_KEYWORDS = new Set([
   "readOnly",
   "writeOnly",
   "$comment",
+  // Core keywords that identify or declare rather than assert. `$ref` is
+  // deliberately absent: it applies whatever it points at, which is exactly an
+  // assertion this module cannot see.
+  "$defs",
+  "$id",
+  "$schema",
+  "$anchor",
+  "$dynamicAnchor",
+  "$vocabulary",
 ]);
 
 /** Whether a schema states no assertion at all. */