After the Civil War, Tony Stark, Director of S.H.I.E.L.D., asked Ms. Marvel to lead the Mighty Avengers team. Ms. Marvel had one condition: she wanted a covert strike team that could deal with Super-villains before they became Avengers-level global threats. Stark agreed, and formed Operation: Lightning Storm.
The team was given full autonomy from the normal S.H.I.E.L.D. hierarchy, but was allowed the full use of S.H.I.E.L.D. resources, including senior agents, and a Minicarrier to act as their mobile base. The core team consisted of Ms. Marvel, Agent Locke, Agent Baines, and Agent Sum.
On their first mission, the team busted up an A.I.M. research lab in Anderson, Indiana, responsible for the detonation of a DNA-scrambling bomb. The subsequent actions involved a full battle between various A.I.M. factions in Seattle. The operation proved disastrous, though, leading to Agent Baines' death and Agent Locke's complete loss of Psi abilities. 
S.H.I.E.L.D. offered up replacement agents in the form of new recruits Machine Man and Sleepwalker. Following a failed raid on the Raft prison, the team traveled to Chile, where they broke up a kidnapping and slavery ring led by the Puppet Master.
The team returned to New York, where they were charged with the capture of Ms. Marvel for being a Skrull infiltrator as part of the Secret Invasion. The team captured two Ms. Marvels, and eventually worked out which one was the impostor. However, the impostor self-destructed while imprisoned on the Minicarrier, destroying the carrier and killing most of the team.
- Carol Danvers (Ms. Marvel) - leader
- Agent Locke (retired) - Psi Ops, General action
- Agent Baines (deceased) - Technical
- Agent Sum - Pilot, General action
- Sleepwalker - General action
- Machine Man - Technical, General action
- Doc Farrell (deceased) - Medical support
- S.H.I.E.L.D. Cape-killer team - troops
Transportation: Minicarrier 13
- 6 Operation: Lightning Storm (Earth-616) Members
- 16 Appearances of Operation: Lightning Storm (Earth-616)
- Minor Appearances of Operation: Lightning Storm (Earth-616)
- Media Operation: Lightning Storm (Earth-616) was Mentioned in
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- Team Gallery: Operation: Lightning Storm (Earth-616)