It seems Zinyak is ticked off at you and decided to retaliate by sending in clones of the various gangs from previous games to attack you. If the mission isn't progressing on its own, go back to the HUB and choose the next stage manually. In order to shut down the point where the clones are coming from, you'll need to go to a certain location and toss C.I.D. into the air, since he doesn't have the strength to scan the area and hover at the same time.
Once you toss C.I.D. into the air and he locates the relay point, go to it and destroy it, noting that there's going to be a lot of resistance in the form of enemies there. Do the same to get the location of the second relay, which is located on a platform that's floating in the air.
The third set of relays are all protected with a shield, so C.I.D. tells you to throw him into the generator so he can disable the shields. Use Telekinesis to throw him into the gathering point of the shields, which is the point they all meet. While he's disabling the shields, you must protect him from the enemies that will be approaching.
The last relay is the same as the third set, although there's only one. Clear the area of the enemies first, then toss C.I.D. into the generator. Protect him while he disables the shield, which will be slightly more challenging this time, as a Marauder shows up, which is a giant rolling ball-like thing of destruction. Its main attack is a laser blast that will knock you back, with its main telling point being two lasers coming together.
The weak point of the Marauder is behind it, so C.I.D. will help out by distracting it. It's best to use your heavy weaponry to whittle its health down. Once it's finished, throw C.I.D. back into the generator so he can finish disabling it. When the shield is gone, destroy the relay and now it's time to track down the source of the gang clones.
Once you get there, use Telekinesis to throw the clones back into the portal, which will begin lowering the health of the portal. On two separate occasions, throwback clones will come out of the portal. Note that these clones have superpowers, so bring their health down to the point where you can toss them back into the portal.
After tossing in the last clone, the portal will be destroyed and Kinzie will chime in saying a Warden is coming for you. Instead of wanting to leave as per Kinzie's request, head to the waypoint to fight the Warden. This one can be a little more challenging than usual because of the terrain, so try to keep yourself on the same level as it. Once it's finished, you'll get a new power and go through some training, with the mission ending after that.
