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Shifter re-integrates a few features which were left out of the game, but were later found in the game's source code. For one example, after rescuing Ford Schick from MJ12, he's supposed to appear in Smuggler's hideout - and he even gives you an augmentation upgrade canister.
This makes saving him worth it, but it doesn't actually happen, so in Shifter, it does. Another example is at the airfield's helicopter bay in one of the offices. JC is supposed to overhear a conversation between Lebedev and Tracer Tong in which Tong is telling Lebedev to kill JC, but Lebedev is insisting that JC can be convinced to change sides. This has been moved around since being brought back. Also, Shifter adds a handful of customized weapons, a feature that gives skill points for kills (and a stealth bonus, if applicable, at the end of each level).
Shifter also contains a modified multiplayer game featuring additional selectable player models and a new inventory system. The new system allocates 6 slots to weapons, with each weapon taking up a varying number of slots based on the weapon's size. Due to these and other changes, it is not possible to join unmodified multiplayer servers while Shifter is installed.
Author Yukichigai's mission statement is as follows: Shifter is my attempt at "removing the suck" from Deus Ex, what little of it there is. There are some annoying aspects of the game system, unresolved glitches, and a minor helping of unrealized potential scattered throughout this groundbreaking game. Shifter attempts to address those issues. As one person put it, paraphrased, Shifter doesn't add new content so much as improve the existing content. Shifter makes Deus Ex what it should have been, or at least one interpretation of what it should have been.
- Blackjack - A standard Baton modified by Paul to maximize damage, but still only render enemies unconscious to keep with Paul's personal non-lethal policy. The Baton has been filled with a hard substance of some kind, most likely lead or iron rebar. One of the few new Shifter weapons with almost no disadvantages, the Blackjack is identical to a Baton in every way with the exception of base damage - the Baton having 8, and the Blackjack having 14. It can be found in one of three locations depending on the player's actions: In Paul's apartment during the player's first visit to Hell's Kitchen, on Paul 's dead body in the Majestic 12 base under UNATCO HQ, or in the lobby of the 'Ton on JC's final visit to Hell's Kitchen.
- Boomstick - The first of two new shotguns added in Shifter, the Boomstick is based off the Sawed-Off Shotgun. The biggest difference when compared to the Sawed-Off Shotgun is the base damage, as the Boomstick has 15 projectiles dealing 2 damage each (30 damage total) - while the Sawed-Off Shotgun has 5 projectiles dealing 5 damage each (25 damage total). This high amount of projectiles gives the Boomstick fairly effective mid-range capabilities. Along with the base damage increase, the Boomstick has slightly higher accuracy and rate of fire and slightly reduced recoil and reload time - in comparison with the Sawed-Off Shotgun. This weapon can be found on a table in Jock's apartment on Tonnochi Road in Hong Kong .
- Jock's Pistol - A silenced pistol found next to the Boomstick in Jock's apartment. It has a unique model, consisting of a regular pistol with a silencer attached (regular pistols cannot be silenced). Unfortunately, it is inferior to JoJo's Lo Bruto in every way, despite being found much later in the game.
- Internal Light Anti-Personnel Weapon, or iLaw - A rapid-fire, Assault Shotgun-sized rocket launcher which uses Light Rockets ("L-Rockets") as opposed to normal ones. L-Rockets are the same rockets used by MJ12 Commandos, and as such don't do the same extreme damage as normal rockets or LAMs. The iLaw is found under the Hell's Kitchen MJ12 lab that Ford Schick was held under, but on later visits, is collapsed. The iLaw is under some fallen rocks. An additional iLaw can be found in VersaLife's Pacific Rim Research Facility in Hong Kong, but only if the player returns after obtaining the Dragon's Tooth Sword's ROM Encoding specifications—specifically, when the facility is much more heavily guarded.
- Jackhammer - The second of two new shotguns added in Shifter, the Jackhammer is based of the Assault Shotgun , as opposed to the Boomstick which is based off the Sawed-Off Shotgun. Created by Smuggler , the Jackhammer has an insanely fast rate of fire, and with one click of the mouse, fires four shotgun shells at once. Shooting 15 projectiles per shell, the Jackhammer uses 4 shells per click, meaning that 60 projectiles in total are shot for each pull of the trigger. Despite its vicious damage output and rate of fire, the Jackhammer has a lengthy reload time of 4.5 seconds, and can chew through the player's ammunition very fast. The Jackhammer is found behind a garage door triggered by laser tripwires in front of Smuggler 's hideout - it only appears in this spot on JC 's final return to Hell's Kitchen .
- Magnum - The Magnum is a powerful variant of the Pistol and uses the same 10mm ammunition. The Magnum's biggest advantage is it's firepower - having a larger base damage than the Pistol , while still only taking up one inventory space can prove to be very efficient. Along with it's higher firepower, the Magnum has increased recoil and is as loud as a Sniper Rifle; silencers are unfortunately incompatible. The Magnum can be found on Juan Lebedev 's bed inside the 747 in LaGuardia Airport.
- Lo Bruto - The Lo Bruto is a modified variant of the standard Stealth Pistol. Modified very poorly by JoJo Fine, the Lo Bruto is his weapon of choice, as it still possesses the stealthy elements of the base weapon while also having a larger base damage. Due to the poor quality of the modification, the higher base damage comes at a cost of a lower clip size, lower reload speed and a higher recoil. This weapon makes for a powerful tool in the hands of a stealthy agent. The Lo Bruto can be obtained by killing or knocking out JoJo Fine, and taking it from his body in the 'Ton Hotel .
- Precision Rifle - A heavily modified sniper rifle, boasting a very low shot time and a blue-tinted high-contrast scope which will highlight visible enemies. It can be found inside the foreman's shack on top of the building where JC makes his first arrival in Paris .
- Prototype Nanoswords, Mark I, II and III. These three swords were previous versions of the mark IV, the Dragon's Tooth Sword. Each occupy 3 squares of inventory space, as opposed to 4 squares of the Dragon's Tooth Sword. The Mark I does the most damage per swing when fully charged, but it also presents the most variance in damage, fluctuating between the uncharged, partially charged, and fully charged states at random; further prototypes reduce max damage but also increase the stability.
- The Mark I can be found in one of two locations, depending on whether or not Paul dies in the raid on the 'Ton: on the unconscious body of Agent Sherman, the Man in Black in charge of the MJ12 base below the UNATCO HQ, or on top of a shipping container near the back entrance to Smuggler's hideout on JC's final return to Hell's Kitchen. Paul also carries this weapon prior to JC's capture by UNATCO, except during the initial mission, and may be seen using it in combat.
- The Mark II can be found on a dead scientist in the sunken tunnels under Hong Kong
- The Mark III can be found in the captain's quarters on board the PRCS Wall Cloud.
- Railgun - A modified Plasma Rifle. Rather than firing normal plasma projectiles, it fires a powerful hitscan projectile that can penetrate walls. It also comes with a scope that allows the user to see targets through walls. It can be found in the house of a weapon smuggler in the Champs-Élysées in Paris. It can also be taken off of Walton Simon's unconscious or dead body at Area 51 if the player is able to defeat him.
- Toxin Blade - A standard Combat Knife coated with paralytic toxins. Utilising nanobot technology, this knife has a self-replenishing system using nanobots to ensure the blade is coated with the deadly poison, even after use. Much like the Riot Prod , the Toxin Blade will paralyse enemies when hit head-on, but from behind or on the head will count as a kill; enemies will also bleed after being hit. The Toxin Blade can be found underneath a pillow on a bed in Smuggler's hideout upon JC's first visit to Hell's Kitchen .
- Shifter adds a touch of realism to the game by introducing random loot. Thanks to this feature, it is possible to obtain a sword as early as on Liberty Island. Weapon mods aren't uncommon either, and one can even find a few of the coveted augmentation upgrade canisters on bodies.
- The mod alters the damage values of some weapons. For example, the crowbar's damage is set to 12 (unmodded Deus Ex had it at 6) in order to justify its 2-square inventory size. The sword has its damage doubled from 10 to 20, the stealth pistol increased from 8 to 12 and the baton from 7 to 8. Also, the one-shot PS20 has its damage tripled from 25 to 75.
- Several new types of ammo appear in the game, most notably the 10mm Explosive Ammo which greatly enhances the usefulness of handheld firearms and the Dragon's Breath Shells for the Shotguns, which upon firing expel a stream on fire that sets any target ablaze.
- Another weapon modification is introduced: the Rate of Fire mod. Typically found on NPC bodies and select locations such as the UNATCO armory. This mod increases the rate of fire of most firearms and rifle weapons by 10% of their base value.
- Many weapons now possess "alt-fire" mode. For example, most melee weapons like knives, crowbars or batons can be thrown at enemies for damage, the Sawed-Off Shotgun's chamber can be loaded with multiple shells to fire them in rapid succession and the Flamethrower can eject its whole napalm canister set ablaze, to produce a strong explosion.
- A mostly aesthetic change, cats now have their behavior altered to seem more natural, e.g. hunting rats and pigeons. This can be observed well in the Mole People Tunnels and Tonnochi Road in Hong Kong.
- NPCs are now capable of acquiring weapons that lie on the ground of their own initiative, This can cause pretty hilarious situations like in the UNATCO HQ.
- In a minor change, Paul Denton no longer carries a plasma rifle on his first appearance on Liberty Island. Instead, he carries nonlethal weapons which are in character for him, like the Pepper Gun.
- The Medicine Skill now allows the agent to make more efficient use of food and beverages for healing. This bonus also applies to watercoolers and water fountains (While in unmodded Deus Ex they heal 1 health point per drink, in Shifter heal from 1 for Untrained to 4 for Master).
- Shifter subjects the Augmenation system to much change:
- Augmentations can now be upgraded not only by using upgrade canisters, but also generic canisters containing the same augmentation you wish to upgrade.
- It is now possible to replace installed augmentations with new ones if all your slots are full. It is done with the help of a Medical Bot, just as if installing a new augmentation normally. It is possible to replace any augmentation in any given body region provided that you have a desirable canister (e.g. replace Power Recirculator with Regeneration). The new augmentation will also keep its Tech Level.
- The Light Augmentation now has four Techs and can be upgraded for increased luminescence.
- The Microfibral Muscle arm aug now also gives the benefits of Combat Strength as well, while Combat Strength is replaced by Electrostatic Discharge, which allows the agent to alter the AI and eventually disable bots with melee weapons.
- The Synthetic Heart augmentation can now increase the performance of most augs even beyond Tech Four, making it a choice worth considering.
- As a tribute to a long-running joke, a new Cranial aug is introduced: the Skull Gun. It can be obtained in two places: first from the vending machine during your escape from the UNATCO HQ (it got mixed up during delivery with a can of lemon-lime soda). The second canister is left behind by Gunther Hermann's corpse in Paris. The canister contains Skull Gun along with another random augmentation, so with luck it is possible to have both Power Recirculator and Synthetic Heart simultaneously.
- Shifter requires only that the player be using either the Deus Ex: Game of the Year Edition (often referred to as GOTY) or the retail version of the game with the 1.112fm patch, which can be downloaded at the Eidos site or various other game file hosts. It includes two files, DEUSEX.U and DEUSEX.INT, and these must replace the ones in the DeusEx\System folder. These must be backed up or moved to another location if you wish to remove Shifter without reinstalling the game. Replacing the files with the ones in the Shifter download will upgrade Deus Ex to Deus Ex with Shifter.
- Shifter also prevents some of the more popular exploits. You will no longer be able to sell your Pistol skill at the beginning for 1250 more skill points. You will no longer be able to use one lockpick and go into the menu. And you shouldn't be able to keep getting 100 skill points by using the switches at Vandenberg. Enabling cheats disables these bug fixes, however.
- Old, pre-Shifter save games are compatible with Shifter, but going vice versa is not compatible.
- There is a bug in Shifter that causes Walton Simons to not use the Agressive Defense System. Also, although not a bug, when you meet him for the first time, he has a Plasma Rifle, If you let him live and meet him again at Area 51, then he has a Railgun.