How do you get Deoxys in Pokemon Ranger?

When you complete the main plot of the game and reach Rank 10, you unlock the feature Ranger Net. This is accessable from the Ranger start menu. Ranger Net begins with the mission "Gain Deoxys's Trust?!". Select this mission.

You will appear in the Ringtown ranger base and Spenser will give you the mission breif. You need to go to the Krokka Tunnel to capture Deoxys. It will change forms each time you try to capture it. You may only do so, however, when it is in the Normal form. To achieve this, you must chase Deoxys through the Krokka Tunnel.

Deoxys isn't that hard to capture. You should easily paralyse it with Plusle or Minun's electrical PokeAssist and loop circles around it. You should also be aware that Deoxys' Speed Forme is very fast and will most definitely require you to use a PokeAssist.