I had already defeated Olympia in Anistar, then I got a strange Holo Clip from Lysander. I didn’t understand what he meant, so I just carried onto the gate. But two men blocked it saying a Pokémon is rampaging near that area. How do I progress?
You're supposed to fly to Lumiose City.
They won't let you any further unless you fly to Lumiose City, beat Lysandre and all of the other grunts, fly to Geosenge Town and catch the Legendary Pokemon.
Hope I helped!