diff --git a/openpype/plugins/publish/collect_scene_loaded_versions.py b/openpype/plugins/publish/collect_scene_loaded_versions.py
new file mode 100644
index 0000000000..199a467dec
--- /dev/null
+++ b/openpype/plugins/publish/collect_scene_loaded_versions.py
@@ -0,0 +1,61 @@
+
+import pyblish.api
+
+
+class CollectSceneLoadedVersions(pyblish.api.ContextPlugin):
+
+    order = pyblish.api.CollectorOrder + 0.0001
+    label = "Collect Versions Loaded in Scene"
+    hosts = [
+        "aftereffects",
+        "blender",
+        "celaction",
+        "fusion",
+        "harmony",
+        "hiero",
+        "houdini",
+        "maya",
+        "nuke",
+        "photoshop",
+        "resolve",
+        "tvpaint"
+    ]
+
+    def process(self, context):
+        from avalon import api, io
+
+        current_file = context.data.get("currentFile")
+        if not current_file:
+            self.log.warn("No work file collected.")
+            return
+
+        host = api.registered_host()
+        if host is None:
+            self.log.warn("No registered host.")
+            return
+
+        if not hasattr(host, "ls"):
+            host_name = host.__name__
+            self.log.warn("Host %r doesn't have ls() implemented." % host_name)
+            return
+
+        loaded_versions = []
+        _containers = list(host.ls())
+        _repr_ids = [io.ObjectId(c["representation"]) for c in _containers]
+        version_by_repr = {
+            str(doc["_id"]): doc["parent"] for doc in
+            io.find({"_id": {"$in": _repr_ids}}, projection={"parent": 1})
+        }
+
+        for con in _containers:
+            # NOTE:
+            # may have more then one representation that are same version
+            version = {
+                "objectName": con["objectName"],  # container node name
+                "subsetName": con["name"],
+                "representation": io.ObjectId(con["representation"]),
+                "version": version_by_repr[con["representation"]],  # _id
+            }
+            loaded_versions.append(version)
+
+        context.data["loadedVersions"] = loaded_versions
diff --git a/openpype/plugins/publish/integrate_inputlinks.py b/openpype/plugins/publish/integrate_inputlinks.py
new file mode 100644
index 0000000000..fbd8738927
--- /dev/null
+++ b/openpype/plugins/publish/integrate_inputlinks.py
@@ -0,0 +1,90 @@
+
+import pyblish.api
+
+
+class IntegrateInputLinks(pyblish.api.ContextPlugin):
+    """Connecting version level dependency links"""
+
+    order = pyblish.api.IntegratorOrder + 0.2
+    label = "Connect Dependency InputLinks"
+
+    def process(self, context):
+        workfile = None
+        publishing = []
+
+        for instance in context:
+            version_doc = instance.data.get("versionEntity")
+            if not version_doc:
+                self.log.debug("Instance %s doesn't have version." % instance)
+                continue
+
+            version_data = version_doc.get("data", {})
+            families = version_data.get("families", [])
+            self.log.debug(families)
+
+            if "workfile" in families:
+                workfile = instance
+            else:
+                publishing.append(instance)
+
+        if workfile is None:
+            self.log.warn("No workfile in this publish session.")
+        else:
+            workfile_version_doc = workfile.data["versionEntity"]
+            # link all loaded versions in scene into workfile
+            for version in context.data.get("loadedVersions", []):
+                self.add_link(
+                    link_type="reference",
+                    input_id=version["version"],
+                    version_doc=workfile_version_doc,
+                )
+            # link workfile to all publishing versions
+            for instance in publishing:
+                self.add_link(
+                    link_type="generative",
+                    input_id=workfile_version_doc["_id"],
+                    version_doc=instance.data["versionEntity"],
+                )
+
+        # link versions as dependencies to the instance
+        for instance in publishing:
+            for input_version in instance.data.get("inputVersions") or []:
+                self.add_link(
+                    link_type="generative",
+                    input_id=input_version,
+                    version_doc=instance.data["versionEntity"],
+                )
+
+        self.write_links_to_database(context)
+
+    def add_link(self, link_type, input_id, version_doc):
+        from collections import OrderedDict
+        from avalon import io
+        # NOTE:
+        # using OrderedDict() here is just for ensuring field order between
+        # python versions, if we ever need to use mongodb operation '$addToSet'
+        # to update and avoid duplicating elements in 'inputLinks' array in the
+        # future.
+        link = OrderedDict()
+        link["type"] = link_type
+        link["input"] = io.ObjectId(input_id)
+        link["linkedBy"] = "publish"
+
+        if "inputLinks" not in version_doc["data"]:
+            version_doc["data"]["inputLinks"] = []
+        version_doc["data"]["inputLinks"].append(link)
+
+    def write_links_to_database(self, context):
+        from avalon import io
+
+        for instance in context:
+            version_doc = instance.data.get("versionEntity")
+            if version_doc is None:
+                continue
+
+            input_links = version_doc["data"].get("inputLinks")
+            if input_links is None:
+                continue
+
+            io.update_one({"_id": version_doc["_id"]},
+                          {"$set": {"data.inputLinks": input_links}})