diff --git a/changelog.d/13004.misc b/changelog.d/13004.misc
new file mode 100644
index 0000000000..d8e93d87af
--- /dev/null
+++ b/changelog.d/13004.misc
@@ -0,0 +1 @@
+Faster joins: add issue links to the TODO comments in the code.
diff --git a/synapse/handlers/federation.py b/synapse/handlers/federation.py
index 6a143440d3..5e16139626 100644
--- a/synapse/handlers/federation.py
+++ b/synapse/handlers/federation.py
@@ -545,6 +545,7 @@ class FederationHandler:
             if ret.partial_state:
                 # TODO(faster_joins): roll this back if we don't manage to start the
                 #   background resync (eg process_remote_join fails)
+                #   https://github.com/matrix-org/synapse/issues/12998
                 await self.store.store_partial_state_room(room_id, ret.servers_in_room)
 
             max_stream_id = await self._federation_event_handler.process_remote_join(
@@ -1506,14 +1507,17 @@ class FederationHandler:
         # TODO(faster_joins): do we need to lock to avoid races? What happens if other
         #   worker processes kick off a resync in parallel? Perhaps we should just elect
         #   a single worker to do the resync.
+        #   https://github.com/matrix-org/synapse/issues/12994
         #
         # TODO(faster_joins): what happens if we leave the room during a resync? if we
         #   really leave, that might mean we have difficulty getting the room state over
         #   federation.
+        #   https://github.com/matrix-org/synapse/issues/12802
         #
         # TODO(faster_joins): we need some way of prioritising which homeservers in
         #   `other_destinations` to try first, otherwise we'll spend ages trying dead
         #   homeservers for large rooms.
+        #   https://github.com/matrix-org/synapse/issues/12999
 
         if initial_destination is None and len(other_destinations) == 0:
             raise ValueError(
@@ -1543,9 +1547,11 @@ class FederationHandler:
                 # all the events are updated, so we can update current state and
                 # clear the lazy-loading flag.
                 logger.info("Updating current state for %s", room_id)
+                # TODO(faster_joins): support workers
+                #   https://github.com/matrix-org/synapse/issues/12994
                 assert (
                     self._storage_controllers.persistence is not None
-                ), "TODO(faster_joins): support for workers"
+                ), "worker-mode deployments not currently supported here"
                 await self._storage_controllers.persistence.update_current_state(
                     room_id
                 )
@@ -1559,6 +1565,8 @@ class FederationHandler:
                     )
 
                     # TODO(faster_joins) update room stats and user directory?
+                    #   https://github.com/matrix-org/synapse/issues/12814
+                    #   https://github.com/matrix-org/synapse/issues/12815
                     return
 
                 # we raced against more events arriving with partial state. Go round
@@ -1566,6 +1574,8 @@ class FederationHandler:
                 # TODO(faster_joins): there is still a race here, whereby incoming events which raced
                 #   with us will fail to be persisted after the call to `clear_partial_state_room` due to
                 #   having partial state.
+                #   https://github.com/matrix-org/synapse/issues/12988
+                #
                 continue
 
             events = await self.store.get_events_as_list(
@@ -1588,6 +1598,7 @@ class FederationHandler:
                             #   indefinitely is also not the right thing to do if we can
                             #   reach all homeservers and they all claim they don't have
                             #   the state we want.
+                            #   https://github.com/matrix-org/synapse/issues/13000
                             logger.error(
                                 "Failed to get state for %s at %s from %s because %s, "
                                 "giving up!",
diff --git a/synapse/handlers/federation_event.py b/synapse/handlers/federation_event.py
index 87a0608359..9889d1cb44 100644
--- a/synapse/handlers/federation_event.py
+++ b/synapse/handlers/federation_event.py
@@ -532,6 +532,7 @@ class FederationEventHandler:
                 #
                 # TODO(faster_joins): we probably need to be more intelligent, and
                 #    exclude partial-state prev_events from consideration
+                #    https://github.com/matrix-org/synapse/issues/13001
                 logger.warning(
                     "%s still has partial state: can't de-partial-state it yet",
                     event.event_id,
@@ -777,6 +778,7 @@ class FederationEventHandler:
             state_ids = await self._resolve_state_at_missing_prevs(origin, event)
             # TODO(faster_joins): make sure that _resolve_state_at_missing_prevs does
             #   not return partial state
+            #   https://github.com/matrix-org/synapse/issues/13002
 
             await self._process_received_pdu(
                 origin, event, state_ids=state_ids, backfilled=backfilled
diff --git a/synapse/handlers/message.py b/synapse/handlers/message.py
index f455158a2c..294217cc23 100644
--- a/synapse/handlers/message.py
+++ b/synapse/handlers/message.py
@@ -1102,6 +1102,7 @@ class EventCreationHandler:
             #
             # TODO(faster_joins): figure out how this works, and make sure that the
             #   old state is complete.
+            #   https://github.com/matrix-org/synapse/issues/13003
             metadata = await self.store.get_metadata_for_events(state_event_ids)
 
             state_map_for_event: MutableStateMap[str] = {}
diff --git a/synapse/storage/controllers/persist_events.py b/synapse/storage/controllers/persist_events.py
index 4caaa81808..4bcb99d06e 100644
--- a/synapse/storage/controllers/persist_events.py
+++ b/synapse/storage/controllers/persist_events.py
@@ -388,10 +388,13 @@ class EventsPersistenceStorageController:
 
         # TODO(faster_joins): get a real stream ordering, to make this work correctly
         #    across workers.
+        #    https://github.com/matrix-org/synapse/issues/12994
         #
         # TODO(faster_joins): this can race against event persistence, in which case we
         #    will end up with incorrect state. Perhaps we should make this a job we
-        #    farm out to the event persister, somehow.
+        #    farm out to the event persister thread, somehow.
+        #    https://github.com/matrix-org/synapse/issues/13007
+        #
         stream_id = self.main_store.get_room_max_stream_ordering()
         await self.persist_events_store.update_current_state(room_id, delta, stream_id)
 
diff --git a/synapse/storage/controllers/state.py b/synapse/storage/controllers/state.py
index 3b4cdb67eb..d3a44bc876 100644
--- a/synapse/storage/controllers/state.py
+++ b/synapse/storage/controllers/state.py
@@ -452,6 +452,9 @@ class StateStorageController:
                  up to date.
         """
         # FIXME(faster_joins): what do we do here?
+        #   https://github.com/matrix-org/synapse/issues/12814
+        #   https://github.com/matrix-org/synapse/issues/12815
+        #   https://github.com/matrix-org/synapse/issues/13008
 
         return await self.stores.main.get_partial_current_state_deltas(
             prev_stream_id, max_stream_id
diff --git a/synapse/storage/databases/main/room.py b/synapse/storage/databases/main/room.py
index 68d4fc2e64..5760d3428e 100644
--- a/synapse/storage/databases/main/room.py
+++ b/synapse/storage/databases/main/room.py
@@ -1112,6 +1112,7 @@ class RoomWorkerStore(CacheInvalidationWorkerStore):
         # this can race with incoming events, so we watch out for FK errors.
         # TODO(faster_joins): this still doesn't completely fix the race, since the persist process
         #   is not atomic. I fear we need an application-level lock.
+        #   https://github.com/matrix-org/synapse/issues/12988
         try:
             await self.db_pool.runInteraction(
                 "clear_partial_state_room", self._clear_partial_state_room_txn, room_id
@@ -1119,6 +1120,7 @@ class RoomWorkerStore(CacheInvalidationWorkerStore):
             return True
         except self.db_pool.engine.module.DatabaseError as e:
             # TODO(faster_joins): how do we distinguish between FK errors and other errors?
+            #   https://github.com/matrix-org/synapse/issues/12988
             logger.warning(
                 "Exception while clearing lazy partial-state-room %s, retrying: %s",
                 room_id,
diff --git a/synapse/storage/databases/main/state.py b/synapse/storage/databases/main/state.py
index 5e6efbd0fc..9674c4a757 100644
--- a/synapse/storage/databases/main/state.py
+++ b/synapse/storage/databases/main/state.py
@@ -435,6 +435,7 @@ class StateGroupWorkerStore(EventsWorkerStore, SQLBaseStore):
         )
 
         # TODO(faster_joins): need to do something about workers here
+        #   https://github.com/matrix-org/synapse/issues/12994
         txn.call_after(self.is_partial_state_event.invalidate, (event.event_id,))
         txn.call_after(
             self._get_state_group_for_event.prefill,
diff --git a/synapse/storage/state.py b/synapse/storage/state.py
index 96aaffb53c..af3bab2c15 100644
--- a/synapse/storage/state.py
+++ b/synapse/storage/state.py
@@ -546,6 +546,7 @@ class StateFilter:
         #  the sender of a piece of state wasn't actually in the room, then clearly that
         #  state shouldn't have been returned.
         #  We should at least add some tests around this to see what happens.
+        #  https://github.com/matrix-org/synapse/issues/13006
 
         # if we haven't requested membership events, then it depends on the value of
         # 'include_others'