Carol Danvers Is Not In On the Secret: Captain Marvel #4 – August, 1968
Captain Marvel as Dr. Lawson receives a call from the Cape to come back. Then we switch to Carol and another person. He tells her that he hopes that Dr. Lawson got the call and she says that she hopes so too, and that she "still a few questions [she'd] like to ask him… about his papers." She still doesn't trust him.
We find out that there is a secret missile launch. It's so secret that General Bridges didn't even tell his head of security. The good reason that he gives is that they are launching deadly bacteria to outer space to see how it react to cosmic rays. If such a description would be made public, as Dr. Lawson points out, it will cause a public panic. But I fail to see the connection between public panic and the head of security making the necessary preparations
Colonel Yon-Rogg makes the missile change its course back to earth as part of a secret plan to see how humans deal with such a crisis. This causes the missile to land in the ocean near New York.
General Bridges flies to the crashing site with Dr. Lawson and Danvers. They have 5 hours before the bacteria are released into the water.
They land in New-York and get on a ship. While sailing towards the missile crasing site, they notice the Sub-Mariner swimming their way. Danvers turns to ask Dr. Lawson if he thinks that the Sub-Mariner had anything to do with the missile, but Dr. Lawson is already gone, and she notices the strange disappearance.
Yon-Rogg has commands Captain Marvel to let no one stop the spreading of the bacteria. That means Captain Marvel has to stop the Sub-Mariner who wants to help the humans. There is a problem however, Sub-Mariner is much stronger then Mar-Vell. Yet by using his wit Mar-Vell makes them both hit the missile which makes it explode.
The issue ends with Sub-Mariner presumably dead, the virus presumably unleashed and Mar-Vell in inner torment.
Again, we see that Carol Danvers is an important figure in the base, but the fact that the General kept such an event a secret from her shows that he doesn't value her opinion or her work much.