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Supply Run is the fortieth main mission in Marvel's Spider-Man. With the antidote taken to counteract Scorpion's poison, players are free to explore the city for a short amount of time before Spider-Man decides it is a good idea to visit Aunt May at F.E.A.S.T. to see how she is doing. Players can use the map to fast travel to the shelter.

As Peter, players visit Aunt May, who appears to be sick. He attempts to contact Miles Morales, who has been sent to retrieve more medical supplies.

Players take on the role of Miles, who is down near the waterfront. Thugs are in the area, and players must sneak around them, making use of the hacking app to distract them. As players successfully locate the antibiotics, Rhino bursts onto the scene, disabling the Sable International soldiers and interrogating them about their supply routes. Scorpion arrives to assist with the questioning; when he stabs one of the men with his tail, Miles runs, knocking over a toolbox in his haste.

Rhino is sent to track down the source of the noise, and players must take the time to stealth-evade him. Most paths require players to sneak very close to Rhino, so patience is key.

Once Miles escapes, he runs into some escaped convicts who are trying to mug a man. He intervenes, fighting one of them. Players do not get to participate.