omega navis

Ok there's a few things you need to do before you can face the omega versions, I'm just going to go over it all just in case you missed something:

-you need to face their Alpha image data first (the solid ones you see within the net after you beat their according liberation mission) with the exception to Protoman/Colonel since they don't have one (but you do need to Liberate the Undernet )

-then once you do you need to beat their Beta versions within the net, they all have specific spots for you to face them but you can't see them, you'll know you found them when you just stop stop running for a second and then you go into a "random battle". Their locations are as follows:
Magnetman/Knightman - ACDC-1, the square right next to the portal to Lan's PC
Gyroman/Shadowman - Oran-1, on the bottom level, a small side path from the main road, the chip dealer on the top level should be in sight
Napalmman/Tomahawkman - SciLab-4, in the big square to the far top left of the map
Searchman/Numberman - End-3, this one is a little hard to describe so bare with me. It's on the far bottom of the map on a little path that extends out right next to the stairs that go to top level.
Meddy/Toadman - End-4, go as far to the right of the map as possible, it's the small path, NOT THE SQUARE
Protoman/Colonel - Undernet-3, also go as far to the right to the map as possible, it should be at the top of that square.

- aaaand finally HOW TO FACE THE OMEGA VERSIONS. Assuming you followed the steps as followed, the Omega versions should be on the map where their Beta versions were, but as an actual random battle. The best thing you should do to face them a lot faster without the hassle of having to run into like 20 weak viruses before you find the Omega version. Is to have a SneakRun subchip active (or maybe the SneakRun program too? Not sure since I haven't tested it out myself) and then just randomly run around that map until A) you find them, or B) the SneakRun subchip expires.

Good luck on the DS navi's