You have to lower the barriers protecting the reactors. The switches are on the wall with the entrance to the pod chamber. Once both reactor barriers are lowered, you need to place spacesuit bombs on them. Once both are successfully placed, there will be a message telling you that this has happened. You are then free to leave the building and star the Duke’s Buccaneers storyline. If you leave at any time after stealing the cocoons but before successfully placing the explosives it will start the Paranid Unification storyline.

If you did successfully start the Duke’s Buccaneers storyline then the up coming battle will be you, the duke and Duke’s Buccaneers fighting the Paranid and HOP forces. If you went the Paranid Unification storyline then it will be you, the duke, Paranid and HOP forces against Duke’s Buccaneers.