Deoxys has been living under the shadows of Deoxys-A and is labeled as "outclassed" due to the fact that Deoxys-A has 30 more base points in the physical and special departments than Deoxys. However, Deoxys can still be an asset in the lead position with a little adjustment in the EVs. There are plenty of EV investments you can play around with to benefit from its defensive stats (even if they're rather miserable). It's important to note that outside of the lead position, it is completely useless, outside of the odd revenge kill with ExtremeSpeed (watch out for Stealth Rock chipping away at the remainder of its health though), so you're better off setting up Spikes as much as you can before it dies. Overall, Deoxys is not entirely outclassed by its other form; it is an asset on any team that requires a reliable lead.
Deoxys is a natural candidate for a suicide lead because of its fantastic Speed; it is only outpaced by its fellow form Deoxys-S. At first glance, this may seem outclassed by Deoxys-S, but surprisingly, this set is capable of handling other leads. Despite having miserable Defense, a couple of EVs invested into Defense can give Deoxys enough bulk to take hits from opposing leads. Shadow Ball is your main attacking option, which can deal with opposing Deoxys-S leads. With the EVs invested, it is capable of scoring a 2HKO with a Shadow Ball followed by ExtremeSpeed. If Deoxys-S uses Taunt, use Shadow Ball and follow it up with ExtremeSpeed to score an OHKO, preventing it from laying down any entry hazards. If Deoxys-S decides to go for the kill, Deoxys is capable of surviving 2 ExtremeSpeeds. Deoxys has a higher chance than Deoxys-S in defeating opposing Deoxys-S leads who invest 252 HP EVs. The last two slots provide entry hazards for the entire team, and works great on hyper offense teams that enjoy entry hazards being deployed early.Team Options & Additional Comments >>>
Focus Sash + Calm Mind is very useful to get two potential Calm Minds — one on the switch, another on the attack — before you sweep. Ice Beam helps special Deoxys hit Dragon- and Flying-type Pokemon for super effective damage. For the Choice Band version, there's also Rock Slide for the Flying-types — especially Ho-Oh. Pursuit is an option for the Choice Bander. If you can get in on the Latias or Latios (after death or support move not called Thunder Wave/Substitute), you can KO them with this if they run off predicting Ice Punch. Deoxys can try using Trick on the Choice sets; however, you are usually just better off using that turn to attack.
A set that runs Focus Sash in conjunction with Counter or Mirror Coat is available. It can nab a couple of surprise KOs, however, the abundance of Stealth Rock and Spikes in the Uber tier means that this set will be really difficult to execute. This is better for starting matches, so entry hazards don't hinder you, but you're better off using the Lead set provided.
One remarkable option is a "SubPetaya" set, which uses Substitute and Petaya Berry, and allows you to take advantage by blocking status and priority moves. Unfortunately, this kind of tactic is better off being used by Deoxys-A, who is more effective at offense than Deoxys.
Checks and Counters
Deoxys must be beaten by prediction and combinations of Pokemon to switch in and resist its attacks. Some Pokemon deserve special mention: Latias wags her finger at Grass Knot, Superpower and Thunder, OHKOes it with Dragon Pulse, and Recovers off the residual damage. If Latias sacrifices Speed EVs in favor of HP and more Special Defense, it can easily survive two Shadow Balls from Deoxys. Forretress takes Superpower, Shadow Ball and Grass Knot like a real man, but it always gets 2HKOed by Thunder or Thunderbolt. Rayquaza resists Superpower and Grass Knot, but is 2HKOed by Shadow Ball, Thunder (which is 70% accurate against Rayquaza, though) or Thunderbolt. Rayquaza also has to watch out for Ice Beam, Ice Punch and Rock Slide. However, by Rayquaza's very presence, Deoxys trembles; Rayquaza is extremely capable of OHKOing with ExtremeSpeed. Ho-Oh's Defense makes Deoxys' Superpower underpowered against the great phoenix, and its great Special Defense can make Deoxys not so special if Deoxys doesn't have an Electric-type move. Spiritomb is immune to Superpower and Psycho Boost, and takes little from Grass Knot. It can then Pursuit or Sucker Punch the Deoxys away.
Dugtrio, while its chances of safely switching in successfully are abysmal, traps Deoxys and OHKOes Deoxys with Sucker Punch, provided the Deoxys attacks; however, you must be warned that ExtremeSpeed has the same priority as Sucker Punch, so Deoxys will move first with its higher Speed stat. Metagross Pursuits Deoxys to death if Deoxys doesn't 2HKO it first. Switching in Metagross is less dangerous than switching in Dugtrio, though, thanks to resisting Grass Knot and Psycho Boost. The Choice Band version is walled by a combination of Lugia and Forretress, who together resist all of its attacks and are never OHKOed single-handedly by one. Cresselia also works in conjunction, neutral or resistant to everything. A Pursuit Deoxys-S is faster than Deoxys and will survive anything this machine throws at it except for boosted Thunder and Shadow Ball, and forces Deoxys to die unless it has Focus Sash.