For the Nova-5 upgrade you need to go to the top of the Nacht der Untoten bunker. Upon looking to a small room at the end of the building, you can see a small yellow canister laying on a table. You are unable to reach the room yourself, but fortunately you carry the D.I.E. Wonderweapon with which you can suck the canister towards you.
Once you grabbed the canister, head to the Weapons Lab in the underground facility. Put the canister in a white machine standing right of the large blueprint hanging on the wall. A Plaguehound will spawn, kill it near the machine. The canister will now fill itself with the gas from the creature.
Pick it up and head towards the crashed plane. Against the bunker, you will here find a small box, interact and melee with it: You can now pick up the Nova-5 upgrade for the D.I.E.