Secret Invasion #6

This issue says Nick Fury is accompanied by "what's left of the Initiative". Only Proton has died (#3). There are many not shown here but everyone else who left Av:I#15 to fight in New York has been or will be shown as a survivor. Probably many are currently injured.
Shanna's scene is a reminder that she stayed behind to mop up the Skrulls in the Savage Land when Ka-Zar left with the Avengers. Sabra isn't mentioned anywhere else in SI.

Here are the tie-ins:-

Mighty Av #19(p21-22) Marvel Boy sees Captain Marvel falling from space and burning up. He meets the dying body staggering from his impact site.
Black Panther (2005) #40(p6:2-22)-41 BP defeats various Super-Skrulls. Storm is captured by an undiscovered Skrull imposter to force BP to stop fighting. BP refuses but another imposter tasers him. The pair are tortured by the Skrulls to learn how their infiltrators were detected, but devices are discovered implanted in them. They are actually Skrulls who have been manipulated to take the victims' places, and speak recorded messages. BP and Storm kill the commander, and Wakandans wipe out the Skrulls.
SI: X-Men #2(p5-23)-4 Beast wants a tissue sample to create something to use against Super-Skrulls so X-Force and bring back a Skrull corpse. Emma Frost fights a Skrull mind-block. She faces the Skrull Dreamers in their Thought-Wall and wipes them out. Nightcrawler takes the Skrull holy sphere to Beast, which claims that Skrulls and mutants are similar. Hank finds that Skrull cells are continually mutating. He tells Scott that the Legacy Virus will work on Skrulls, but much faster and it would be genocide. The Skrulls use humans as hostages to force the XM to surrender. Cyclops decides to use the Virus and they surrender to various Skrull ships. Cyclops tells the Skrulls they will be dead within a day. He offers them the antidote to leave the city. But the commander destroys the ships to contain the disease. The XM escape.

SI: Inhumans #1(p14-22)-2 Various Inhumans turn out to be Skrulls. Medusa defeats her attacker and forces him to say what happened to Black Bolt. The real BB is a prisoner of the Skrulls, and they hope to use his voice as a weapon. Gorgon stops fighting to protect King Maximus from a Skrull who replaced BB/Medusa's son Ahura. Crystal, Gorgon, Karnak, Medusa and Triton steal a Skrull ship to go find BB. But the Skrulls threaten to torture Ahura to get BB to use his voice for them.
Thunderbolts #125(p1-11) The team continue to fight more Skrulls in Washington, and now bring down the last warship. Norman Osborn plays up to the TV cameras, and is treated like a hero. The last Skrulls take pills which transform them into a giant blob, but Radioactive Man and Songbird combine to kill it. NO and Moonstone don't like those 2. NO benches RM because the Skrulls turned him into a bomb earlier. He tries to rile SB into quitting. Swordsman just wants to kill more of the aliens (he was told) killed his sister. They leave for Manhattan.
Av:I#17-18 There are still some non-Skrulls left at Initiative HQ. Bengal contacts the rest of the Shadow Initiative:- Constrictor, Mutant Zero and Trauma. Ant-Man sees Skrull-Dugan and Veranke arrive, and then gets picked up by Bengal and co who send him with a bomb to blow open a door and then they assassinate Veranke. But that turns out to be a double and the real Skrull Queen makes them suspect Trauma is a Skrull which leads to their defeat. AM is still free and gets evidence of a Skrull backup-plan. Skrull Kill Krew (Komodo, Riot, Ryder and 3-D Man) kill the imposters in Nevada's Heavy Hitters, Utah's The Called, Montana's Freedom Force and Pennsylvania's Liberteens. Cloud 9, Gravity, Hardball, Nonstop and Whiz Kid join them. Meanwhile robot Jocasta leader of New Mexico's Mavericks contacts Devil-Slayer of Hawaii's Point-Men. He uses his cloak to speed up their visits to the Initiative teams, but it weakens him.

Dugan prepares a strike force to hit the Krew when his scientists perfect tracking DS's teleportation. He broadcasts a message to all Initiative teams telling the sleeper agents to reveal themselves to throw the teams into paranoia. The Skrulls detect the Krew arriving at Georgia's Cavalry HQ. AM hitches a ride with the strike force. The Krew see Thor Girl and Ultragirl fighting in midair, too far away for 3-D Man to tell which is a Skrull. Cloud 9 shoots them both. When they crashland Thor Girl is revealed as the imposter. As the Skrulls arrive the Krew retreat with AM who tells them that the Skrulls have rigged the Negative Zone portals in each Initiative base. If they are losing the war the imposters will trigger them to send the US into the Zone. (This was invented by Tony Stark to send Manhattan to the Zone during World War Hulk.) It only requires 3 portals to be successful. We learn that there are only 6 teams the Krew haven't sanitised, but they only have 3 people capable of detecting Skrulls (Riot, Ryder and 3-D Man). Ryder reveals that 3 previous Krew members (Catwalk, Dice and Moonstomp) aren't dead - their heads are preserved in the battle van. He sends 3 speedsters to blow up the Skrull devices in the bases they've already cleansed. Meanwhile the rest will split into 6 teams with a Skrull-detector each. DS sends them away and collapses.
SI: Home Invasion #7-8(p1-9) Pulsar and Sasquatch come to investigate the energy discharges. Kinsey uses the tracker to find her real brother. Pulsar tells K to wait outside while they fight Skrulls and a Super-Skrull which defeats Sasquatch. K sneaks in and uses her force bubble to kill it. But her brother's working *with* the Skrulls. His own wormhole technology will allow them to instantaneously travel anywhere in the Galaxy. K learns that his research is in the building and uses the wristbands to blow it up. But she saves the heroes, and takes Hank away in her bubble.

Captain Britain & MI13 #3-4 Pete Wisdom releases some mystic beings to oppose the demon-powered Skrulls, and gets a shard of the Fury to resurrect Captain Britain who kills the demon. PW also persuades Satannish to banish all Skrulls from Britain.
Incredible Hercules #119-120 Herc's God Squad are in the graveyard of pantheons of races defeated by the Skrulls. The Skrull-coyote pup Kirby transforms into Amadeus Cho to crashland their ship, but Atum sees and exposes him. Members of the other pantheons attack but Atum/Demogorge eats them and Snowbird says she'll hold them off while they escape. The Skrull gods Klyb'n and Sl'gur't attack. Ajak and Atum are killed but so are Klyb'n and Sl'gur't. Herc brings the palace down and Snowbird flies him and Cho to safety. On the Skrull flagship the sacred Book of Worlds self-destructs, and they hear that Mr Fantastic has escaped.
Tb#125(p12-16) The Thunderbolts see Thor's lightning strike in Central Park and head there to join the forces and the battle.
SI: Front Line #4(p18-21)-5(p1-5:1) Ben Urich and Melanie Crane leave Avengers Tower. Bill Dawson and Lisa Carter stay with Jonathan Bryant who dies. Ben and Melanie see Thor's lightning and witness the start of the battle.
A:I#19(p1-10) Believing that 3-D Man is the only 1 who can detect Skrulls, Skrull-Dugan sends his strike force to Texas while the SKK deinfest the Arkansas Battalion, Kentucky Action Pack, Wisconsin Great Lakes Initiative, Florida Command and Washington Earth Force. In the Texas Rangers the Skrull infiltrator turns out to be Red Wolf's wolf Lobo. Skrull agitators turn the crowd against 3-D Man whose goggles get broken so he can't tell who's a Skrull, but he finds that his tri-force energy means he doesn't *need* the goggles. We see Initiative members Crusader, Gauntlet and Taskmaster in the Central Park battle. Nonstop arrives to blow up the whole New Mexico Mavericks' base.