During the construction of the Sodor Search and Rescue Centre, Sir Topham Hatt decided to build his new office inside the old tunnel, but Whiff insisted that it was not a good idea as it connects to Misty Island. When Percy saw Thomas' smoke signals coming from Misty Island, Whiff and Percy used the old tunnel to find Thomas and the Logging Locos. Afterwards, Misty Island Tunnel was restored and officially reopened. It was the most common way for the engines to travel between the two islands.
- Strangely the tunnel was briefly re-boarded up, as seen in The Thomas Way and Too Many Fire Engines.
- Additionally the tunnel entrance is missing in Steam Team to the Rescue. The track leading to the tunnel is still visible, but leads nowhere.