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Roy Halladay left Sunday’s game after pitching just two innings, due to shoulder soreness. Phillies Nation is holding their collective breaths until at least Tuesday, when Halladay is scheduled to seek a medical examination and opinion.

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After losing four games in a row at home, two each to the Red Sox and Nationals, the Phillies righted their ship for a while, avoiding a sweep at the hands of the Nats, then reeling off three straight wins at St. Louis.

The attempt at the sweep failed miserably, with an 8-3 loss.

The biggest news out of that loss was not the first inning grand slam that Roy Halladay gave up to Yadier Molina, but the fact that Halladay left the game after two innings with shoulder soreness.

Not surprisingly, Halladay said that he had been dealing with soreness for a while – but says this latest bout developed during his Tuesday start against Washington. The exact origin, however, was a point of disagreement between Halladay and pitching coach Rich Dubee. Dubee said “Yeah, it’s been an issue. It’s been there. It’s been lingering. Some days it’s better than others. [At] Chicago [two starts ago. it] was better than others. Even the start of last game [against Washington] it was better and then got it cranky. Today, warming up, he felt fine, but as he got into the game and sat down and even before the first inning, it was just hard to get it going again.”

After I questioned last week on Phillies Notebook whether the team was being less than candid about a now-you-see-it, now-you-don’t knee injury to Chad Qualls, this whole Halladay scenario is becoming a high-stakes, extended play version of the same song. Throw in the way Phillies’ beat writer Bob Brookover was treated when trying to watch Ryan Howard‘s rehab on a field in Clearwater (he was order to leave on two different occasions), and we might even have the makings of a full-fledged conspiracy.

Consider this:

1. During spring training, it was widely reported that Halladay’s velocity was down, as his ERA ballooned to 10.57. When asked about this issue, Halladay said the following:

“Yeah, I heard about that … poor reporting on the extreme end of poor reporting. It couldn’t be further from the truth…[Y]eah, I’m 34 and 2500 (career major league) innings, it does take a while to get going. I don’t pay attention to that (velocity). The older you get, the more you throw, the longer it takes to get yourself going.”

2. After wrapping up spring training on a positive note, Halladay dominated for 8 innings on Opening Day, a 1-0 win at Pittsburgh, and went 3-2 with a 1.95 ERA in April. In May, which started off with the 15-13 loss at Atlanta – a game where Halladay gave up 8 runs on 12 hits in 5-1/3 innings – his ERA is 6.11.

Even more telling, Halladay allowed no home runs and less than one hit per inning in each of his 5 April starts. In May, Halladay has allowed 6 home runs, including 5 in his last 3 starts, and more than one hit per inning in 3 of his 6 starts.

3. There was also the departure from the team after the May 2 game in Atlanta for personal reasons. While the reasons reportedly had nothing to do with his physical health, they may be contributing to a lack of complete focus on pitching.

Halladay has another year (2013) remaining on his contract at $20 million, along with a vesting option for 2014 at another $20 million, which kicks in with 415 combined innings in 2012-2013. If Halladay is on the shelf for an extended period of time in 2012, such that he doesn’t reach 190 innings this season, he will have to reach 225 innings in 2013 and finish the 2013 healthy in order to have the option vest.

There are obviously high stakes involved, especially with Vance Worley on the DL and the lineup, bench and bullpen all depleted to one degree or another by injury. If Halladay were to have to miss his next start – which is scheduled for Saturday at home against the Marlins, but could be pushed back to Sunday with Thursday’s off-day, Scott Elarton – one of the Phillies’ feel-good stories from spring training – is the likely candidate to get the call from AAA. Elarton also pitched Sunday, so he is on track to take a weekend start, but he has struggled of late – giving up 10 earned runs in his last 8-2/3 innings, after winning 4 straight games with 1 earned run allowed over 24 innings.

Says here that Halladay will be diagnosed with a strained shoulder – which really amounts to weakness/fatigue in the muscles around his shoulder, back and neck. He will probably need to miss one start, which makes it almost necessary to put him on the DL so as not to wear out the bullpen – especially with Blanton, Kendrick and Elarton in the rotation – each of whom could could have to come out early on any given day.

In the bigger picture, with Halladay turning 37 in his vesting option year of 2014 – in which he may become a free agent – the stark reality is that Cole Hamels is taking over as staff ace. Hamels figures to break the bank with his next contract, which is soon going to put a lot of pressure on Ruben Amaro to make the right calls with how he allocates the team’s payroll going forward – especially with Shane Victorino and Hunter Pence also due to be free agents at the end of this season, and John Mayberry and Domonic Brown not at all looking like either would be a suitable alternative. Then there’s the matter of Carlos Ruiz taking his game to a new level – the $5 million 2013 team option is a no-brainer, but after that, Yadier Molina’s new extension – for 5 years and an average of over $14 million per year – gives you some idea of what a bargain Ruiz has been, and what kind of money he will be aiming for next season.

With all this tumult, it’s ironic that it was widely reported earlier this week that the Roy Halladay bobblehead figurine on sale on MLB.com (which has since been removed from the “shelves”) depicts Halladay throwing left-handed.

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Who stays, who goes? Eventually, Jim Thome (back) – who has been hitting in simulated games in Clearwater, but not playing the field – will be healthy enough to come off the DL, perhaps as a DH when the Phillies play road interleague games in about 10 days. Michael Martinez (foot) will be ready soon. Laynce Nix (calf) is further away – probably in line with Ryan Howard (achilles) and Chase Utley (knee).

Five hitters will have to go somewhere – barring intervening injuries.

Freddy Galvis leads all MLB rookies in RBI with 23, and is tied for third in RBI among all major league second basemen. Galvis’ 18 May RBI are tops among MLB second basemen.

Mike Fontenot is hitting .444 in 17 at-bats. Hector Luna is right behind at .350, with a homer an 6 RBI in only 20 at-bats. John Mayberry has nearly 6 times as many at-bats as Luna (117), but has the same number of homers and only 3 more RBI.

Pete Orr is…well…Pete Orr. Amazingly, Orr has been with the team all season. His versatility and decent fielding is usually what earns him the first call when the injury bug, but his .300 batting average is a pleasant bonus.

Keeping in mind that Mayberry would have to go through waivers to be sent down, he is presumably safe. Fontenot and Luna are in the same boat, though arguably expendable. Orr has options this season, so he is likely the first to go, probably when Thome is activated.

The tough part is that Galvis also has options. It was widely expected that Galvis would go to the minors once Utley was activated, in order to play every day and in order to preserve the bench depth that the Phillies have accrued. But at this point, Galvis’ production and play is simply too good to try to keep a Fontenot or a Luna around.

Conceivably, we might be talking about Chase Utley in left field. While he may not make any spectacular plays out there (and he might in fact be under orders not to go all-out), the Phillies have hidden players with chronic injuries (i.e. Pat Burrell) out there before.

Stay tuned. And remember, if it happens, you heard it here first, on PhillyPhanatics.com.

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Powerful NL East: While the Phillies have stuck their collective heads above the .500 mark on and off throughout the last couple of weeks, they have not managed to climb out of the NL East cellar. At times, the NL East has boasted all five teams holding a winning record. For those who dismissed the talk of the NL East being a competitive division as a way of simply saying the Phillies have fallen back to the pack, it’s becoming clear that each of the Phils’ NL East opponents – even the Mets – have positive attributes.

There is no Pittsburgh, Chicago or San Diego to stomp all over in this division.

The Phillies can get themselves out of last place this week, at the expense of the Mets (who host the Phils Monday-Wednesday) and the Marlins (who play a weekend series at Citizens Bank Park).

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Hard to believe, Harry: With all the attention focused on the big three of Halladay, Lee and Hamels – guess who has the only two complete games of 2012 (both shutouts)? None other than Joe Blanton and Kyle Kendrick.

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Qualls make me queasy: As bad as Halladay’s start was Sunday, the Phillies were showing some signs of life – until Chad Qualls gave up a three-run homer to Carlos Beltran in the 5th, putting the game out of reach at 7-1. It was Qualls 5th home run allowed this season. Four of those homers have come in Qualls’ last five outings, where he has given up 6 runs and 9 hits in 6 innings. Overall, Qualls has retired the side in order just twice in 20 outings.

Let the comparisons with Danys Baez continue. I have heard them a lot recently, but I will take credit for starting them way back on February 14, before Qualls even threw a pitch as a Phillie.

In baseball, numbers rarely lie.

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Contrary to earlier opinions, Contreras may be useful after all: I have been almost as critical of Jose Contreras as of Chad Qualls, though I have always pointed out that Contreras is returning from Tommy John surgery at age 40, less than a year post-op. That is really quick and probably too much to ask.

After sitting with a 9.00 ERA on May 13, Contreras has thrown five straight scoreless outings, lowering his ERA to 5.68. Contreras has only allowed one baserunner in those outings, spanning 4-2/3 innings, with 4 strikeouts.

Simply put, when it comes to the right-handed set up men on the Phillies, it’s Chad Qualls who’s the evil of two lessers.

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